minimap2 0.2.24.6 → 0.2.25.0

checksums.yaml

@@ -1,7 +1,7 @@
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data/ext/minimap2.patch

@@ -1,5 +1,5 @@
---- Makefile.org	2021-05-27 15:45:11.993128205 +0900
-+++ Makefile	2021-05-27 15:46:02.320569154 +0900
+--- a/Makefile
++++ b/Makefile
 @@ -1,9 +1,9 @@
 -CFLAGS=		-g -Wall -O2 -Wc++-compat #-Wextra
 +CFLAGS=		-g -Wall -O2 -Wc++-compat -fPIC #-Wextra
@@ -12,7 +12,7 @@
  PROG=		minimap2
  PROG_EXTRA=	sdust minimap2-lite
  LIBS=		-lm -lz -lpthread
-@@ -130,3 +130,4 @@ sdust.o: kalloc.h kdq.h kvec.h sdust.h
+@@ -134,3 +134,4 @@ sdust.o: kalloc.h kdq.h kvec.h sdust.h
  seed.o: mmpriv.h minimap.h bseq.h kseq.h kalloc.h ksort.h
  sketch.o: kvec.h kalloc.h mmpriv.h minimap.h bseq.h kseq.h
  splitidx.o: mmpriv.h minimap.h bseq.h kseq.h

data/lib/minimap2/aligner.rb

@@ -139,6 +139,7 @@ module Minimap2
     )
 
       return if index.null?
+      return if (map_opt[:flag] & 4).zero? && (index[:flag] & 2).zero?
 
       map_opt[:max_frag_len] = max_frag_len if max_frag_len
       map_opt[:flag] |= extra_flags if extra_flags
@@ -201,6 +202,9 @@ module Minimap2
     # @param stop
 
     def seq(name, start = 0, stop = 0x7fffffff)
+      return if index.null?
+      return if (map_opt[:flag] & 4).zero? && (index[:flag] & 2).zero?
+
       lp = ::FFI::MemoryPointer.new(:int)
       s = FFI.mappy_fetch_seq(index, name, start, stop, lp)
       l = lp.read_int

data/lib/minimap2/ffi/constants.rb

@@ -34,10 +34,12 @@ module Minimap2
     NO_END_FLT       = 0x10000000
     HARD_MLEVEL      = 0x20000000
     SAM_HIT_ONLY     = 0x40000000
-    RMQ              = 0x80000000  # LL
-    QSTRAND          = 0x100000000 # LL
-    NO_INV           = 0x200000000 # LL
-    NO_HASH_NAME     = 0x400000000 # LL
+    RMQ              = 0x80000000
+    QSTRAND          = 0x100000000
+    NO_INV           = 0x200000000
+    NO_HASH_NAME     = 0x400000000
+    SPLICE_OLD       = 0x800000000
+    SECONDARY_SEQ    = 0x1000000000 # output SEQ field for seqondary alignments using hard clipping
 
     HPC              = 0x1
     NO_SEQ           = 0x2
@@ -74,79 +76,6 @@ module Minimap2
         :a, MM128.ptr
     end
 
-    # indexing option
-    class IdxOpt < ::FFI::Struct
-      layout \
-        :k,               :short,
-        :w,               :short,
-        :flag,            :short,
-        :bucket_bits,     :short,
-        :mini_batch_size, :int64_t,
-        :batch_size,      :uint64_t
-    end
-
-    # mapping option
-    class MapOpt < ::FFI::Struct
-      layout \
-        :flag,                 :int64_t, # see MM_F_* macros
-        :seed,                 :int,
-        :sdust_thres,          :int,     # score threshold for SDUST; 0 to disable
-        :max_qlen,             :int,     # max query length
-        :bw,                   :int,     # bandwidth
-        :bw_long,              :int,
-        :max_gap,              :int,     # break a chain if there are no minimizers in a max_gap window
-        :max_gap_ref,          :int,
-        :max_frag_len,         :int,
-        :max_chain_skip,       :int,
-        :max_chain_iter,       :int,
-        :min_cnt,              :int,     # min number of minimizers on each chain
-        :min_chain_score,      :int,     # min chaining score
-        :chain_gap_scale,      :float,
-        :chain_skip_scale,     :float,
-        :rmq_size_cap,         :int,
-        :rmq_inner_dist,       :int,
-        :rmq_rescue_size,      :int,
-        :rmq_rescue_ratio,     :float,
-        :mask_level,           :float,
-        :mask_len,             :int,
-        :pri_ratio,            :float,
-        :best_n,               :int,     # top best_n chains are subjected to DP alignment
-        :alt_drop,             :float,
-        :a,                    :int,     # matching score
-        :b,                    :int,     # mismatch
-        :q,                    :int,     # gap-open
-        :e,                    :int,     # gap-ext
-        :q2,                   :int,     # gap-open
-        :e2,                   :int,     # gap-ext
-        :sc_ambi,              :int,     # score when one or both bases are "N"
-        :noncan,               :int,     # cost of non-canonical splicing sites
-        :junc_bonus,           :int,
-        :zdrop,                :int,     # break alignment if alignment score drops too fast along the diagonal
-        :zdrop_inv,            :int,
-        :end_bonus,            :int,
-        :min_dp_max,           :int,     # drop an alignment if the score of the max scoring segment is below this threshold
-        :min_ksw_len,          :int,
-        :anchor_ext_len,       :int,
-        :anchor_ext_shift,     :int,
-        :max_clip_ratio,       :float,   # drop an alignment if BOTH ends are clipped above this ratio
-        :rank_min_len,         :int,
-        :rank_frac,            :float,
-        :pe_ori,               :int,
-        :pe_bonus,             :int,
-        :mid_occ_frac,         :float,   # only used by mm_mapopt_update(); see below
-        :q_occ_frac,           :float,
-        :min_mid_occ,          :int32,
-        :max_mid_occ,          :int32,
-        :mid_occ,              :int32, # ignore seeds with occurrences above this threshold
-        :max_occ,              :int32,
-        :max_max_occ,          :int32,
-        :occ_dist,             :int32,
-        :mini_batch_size,      :int64_t, # size of a batch of query bases to process in parallel
-        :max_sw_mat,           :int64_t,
-        :cap_kalloc,           :int64_t,
-        :split_prefix,         :string
-    end
-
     # minimap2 index
     class IdxSeq < ::FFI::Struct
       layout \
@@ -173,17 +102,6 @@ module Minimap2
         :h,     :pointer
     end
 
-    # index reader
-    class IdxReader < ::FFI::Struct
-      layout \
-        :is_idx,      :int,
-        :n_parts,     :int,
-        :idx_size,    :int64_t,
-        :opt,         IdxOpt,
-        :fp_out,      :pointer, # FILE
-        :seq_or_idx,  :pointer  # FIXME: Union mm_bseq_files or FILE
-    end
-
     # minimap2 alignment
     class Extra < ::FFI::BitStruct
       layout \
@@ -242,6 +160,90 @@ module Minimap2
                 :dummy,           5
     end
 
+    # indexing option
+    class IdxOpt < ::FFI::Struct
+      layout \
+        :k,               :short,
+        :w,               :short,
+        :flag,            :short,
+        :bucket_bits,     :short,
+        :mini_batch_size, :int64_t,
+        :batch_size,      :uint64_t
+    end
+
+    # mapping option
+    class MapOpt < ::FFI::Struct
+      layout \
+        :flag,                 :int64_t, # see MM_F_* macros
+        :seed,                 :int,
+        :sdust_thres,          :int,     # score threshold for SDUST; 0 to disable
+        :max_qlen,             :int,     # max query length
+        :bw,                   :int,     # bandwidth
+        :bw_long,              :int,
+        :max_gap,              :int,     # break a chain if there are no minimizers in a max_gap window
+        :max_gap_ref,          :int,
+        :max_frag_len,         :int,
+        :max_chain_skip,       :int,
+        :max_chain_iter,       :int,
+        :min_cnt,              :int,     # min number of minimizers on each chain
+        :min_chain_score,      :int,     # min chaining score
+        :chain_gap_scale,      :float,
+        :chain_skip_scale,     :float,
+        :rmq_size_cap,         :int,
+        :rmq_inner_dist,       :int,
+        :rmq_rescue_size,      :int,
+        :rmq_rescue_ratio,     :float,
+        :mask_level,           :float,
+        :mask_len,             :int,
+        :pri_ratio,            :float,
+        :best_n,               :int,     # top best_n chains are subjected to DP alignment
+        :alt_drop,             :float,
+        :a,                    :int,     # matching score
+        :b,                    :int,     # mismatch
+        :q,                    :int,     # gap-open
+        :e,                    :int,     # gap-ext
+        :q2,                   :int,     # gap-open
+        :e2,                   :int,     # gap-ext
+        :sc_ambi,              :int,     # score when one or both bases are "N"
+        :noncan,               :int,     # cost of non-canonical splicing sites
+        :junc_bonus,           :int,
+        :zdrop,                :int,     # break alignment if alignment score drops too fast along the diagonal
+        :zdrop_inv,            :int,
+        :end_bonus,            :int,
+        :min_dp_max,           :int,     # drop an alignment if the score of the max scoring segment is below this threshold
+        :min_ksw_len,          :int,
+        :anchor_ext_len,       :int,
+        :anchor_ext_shift,     :int,
+        :max_clip_ratio,       :float,   # drop an alignment if BOTH ends are clipped above this ratio
+        :rank_min_len,         :int,
+        :rank_frac,            :float,
+        :pe_ori,               :int,
+        :pe_bonus,             :int,
+        :mid_occ_frac,         :float,   # only used by mm_mapopt_update(); see below
+        :q_occ_frac,           :float,
+        :min_mid_occ,          :int32,
+        :max_mid_occ,          :int32,
+        :mid_occ,              :int32, # ignore seeds with occurrences above this threshold
+        :max_occ,              :int32,
+        :max_max_occ,          :int32,
+        :occ_dist,             :int32,
+        :mini_batch_size,      :int64_t, # size of a batch of query bases to process in parallel
+        :max_sw_mat,           :int64_t,
+        :cap_kalloc,           :int64_t,
+        :split_prefix,         :string
+    end
+
+    # index reader
+    class IdxReader < ::FFI::Struct
+      layout \
+        :is_idx,      :int,
+        :n_parts,     :int,
+        :idx_size,    :int64_t,
+        :opt,         IdxOpt,
+        :fp_out,      :pointer, # FILE
+        :seq_or_idx,  :pointer  # FIXME: Union mm_bseq_files or FILE
+    end
+
     # memory buffer for thread-local storage during mapping
     class TBuf < ::FFI::Struct
       layout \

data/lib/minimap2/version.rb

@@ -1,6 +1,6 @@
 # frozen_string_literal: true
 
 module Minimap2
-  #  Minimap2-2.24 (r1122)
-  VERSION = "0.2.24.6"
+  # Minimap2-2.25 (r1173)
+  VERSION = "0.2.25.0"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: minimap2
 version: !ruby/object:Gem::Version
-  version: 0.2.24.6
+  version: 0.2.25.0
 platform: ruby
 authors:
 - kojix2
@@ -87,102 +87,6 @@ files:
 - ext/minimap2/kthread.h
 - ext/minimap2/kvec.h
 - ext/minimap2/lchain.c
-- ext/minimap2/lib/simde/CONTRIBUTING.md
-- ext/minimap2/lib/simde/COPYING
-- ext/minimap2/lib/simde/README.md
-- ext/minimap2/lib/simde/amalgamate.py
-- ext/minimap2/lib/simde/meson.build
-- ext/minimap2/lib/simde/netlify.toml
-- ext/minimap2/lib/simde/simde/arm/neon.h
-- ext/minimap2/lib/simde/simde/arm/neon/float32x2.h
-- ext/minimap2/lib/simde/simde/arm/neon/float32x4.h
-- ext/minimap2/lib/simde/simde/arm/neon/float64x1.h
-- ext/minimap2/lib/simde/simde/arm/neon/float64x2.h
-- ext/minimap2/lib/simde/simde/arm/neon/int16x4.h
-- ext/minimap2/lib/simde/simde/arm/neon/int16x8.h
-- ext/minimap2/lib/simde/simde/arm/neon/int32x2.h
-- ext/minimap2/lib/simde/simde/arm/neon/int32x4.h
-- ext/minimap2/lib/simde/simde/arm/neon/int64x1.h
-- ext/minimap2/lib/simde/simde/arm/neon/int64x2.h
-- ext/minimap2/lib/simde/simde/arm/neon/int8x16.h
-- ext/minimap2/lib/simde/simde/arm/neon/int8x8.h
-- ext/minimap2/lib/simde/simde/arm/neon/uint16x4.h
-- ext/minimap2/lib/simde/simde/arm/neon/uint16x8.h
-- ext/minimap2/lib/simde/simde/arm/neon/uint32x2.h
-- ext/minimap2/lib/simde/simde/arm/neon/uint32x4.h
-- ext/minimap2/lib/simde/simde/arm/neon/uint64x1.h
-- ext/minimap2/lib/simde/simde/arm/neon/uint64x2.h
-- ext/minimap2/lib/simde/simde/arm/neon/uint8x16.h
-- ext/minimap2/lib/simde/simde/arm/neon/uint8x8.h
-- ext/minimap2/lib/simde/simde/check.h
-- ext/minimap2/lib/simde/simde/debug-trap.h
-- ext/minimap2/lib/simde/simde/hedley.h
-- ext/minimap2/lib/simde/simde/simde-arch.h
-- ext/minimap2/lib/simde/simde/simde-common.h
-- ext/minimap2/lib/simde/simde/x86/avx.h
-- ext/minimap2/lib/simde/simde/x86/avx2.h
-- ext/minimap2/lib/simde/simde/x86/avx512bw.h
-- ext/minimap2/lib/simde/simde/x86/avx512f.h
-- ext/minimap2/lib/simde/simde/x86/avx512vl.h
-- ext/minimap2/lib/simde/simde/x86/fma.h
-- ext/minimap2/lib/simde/simde/x86/mmx.h
-- ext/minimap2/lib/simde/simde/x86/sse.h
-- ext/minimap2/lib/simde/simde/x86/sse2.h
-- ext/minimap2/lib/simde/simde/x86/sse3.h
-- ext/minimap2/lib/simde/simde/x86/sse4.1.h
-- ext/minimap2/lib/simde/simde/x86/sse4.2.h
-- ext/minimap2/lib/simde/simde/x86/ssse3.h
-- ext/minimap2/lib/simde/simde/x86/svml.h
-- ext/minimap2/lib/simde/test/CMakeLists.txt
-- ext/minimap2/lib/simde/test/arm/meson.build
-- ext/minimap2/lib/simde/test/arm/neon/meson.build
-- ext/minimap2/lib/simde/test/arm/neon/skel.c
-- ext/minimap2/lib/simde/test/arm/neon/test-neon-internal.h
-- ext/minimap2/lib/simde/test/arm/neon/test-neon.c
-- ext/minimap2/lib/simde/test/arm/neon/test-neon.h
-- ext/minimap2/lib/simde/test/arm/neon/vadd.c
-- ext/minimap2/lib/simde/test/arm/neon/vdup_n.c
-- ext/minimap2/lib/simde/test/arm/neon/vmul.c
-- ext/minimap2/lib/simde/test/arm/neon/vsub.c
-- ext/minimap2/lib/simde/test/arm/test-arm-internal.h
-- ext/minimap2/lib/simde/test/arm/test-arm.c
-- ext/minimap2/lib/simde/test/arm/test-arm.h
-- ext/minimap2/lib/simde/test/cmake/AddCompilerFlags.cmake
-- ext/minimap2/lib/simde/test/cmake/ExtraWarningFlags.cmake
-- ext/minimap2/lib/simde/test/meson.build
-- ext/minimap2/lib/simde/test/munit/COPYING
-- ext/minimap2/lib/simde/test/munit/Makefile
-- ext/minimap2/lib/simde/test/munit/README.md
-- ext/minimap2/lib/simde/test/munit/example.c
-- ext/minimap2/lib/simde/test/munit/meson.build
-- ext/minimap2/lib/simde/test/munit/munit.c
-- ext/minimap2/lib/simde/test/munit/munit.h
-- ext/minimap2/lib/simde/test/run-tests.c
-- ext/minimap2/lib/simde/test/run-tests.h
-- ext/minimap2/lib/simde/test/x86/avx.c
-- ext/minimap2/lib/simde/test/x86/avx2.c
-- ext/minimap2/lib/simde/test/x86/avx512bw.c
-- ext/minimap2/lib/simde/test/x86/avx512f.c
-- ext/minimap2/lib/simde/test/x86/avx512vl.c
-- ext/minimap2/lib/simde/test/x86/fma.c
-- ext/minimap2/lib/simde/test/x86/meson.build
-- ext/minimap2/lib/simde/test/x86/mmx.c
-- ext/minimap2/lib/simde/test/x86/skel.c
-- ext/minimap2/lib/simde/test/x86/sse.c
-- ext/minimap2/lib/simde/test/x86/sse2.c
-- ext/minimap2/lib/simde/test/x86/sse3.c
-- ext/minimap2/lib/simde/test/x86/sse4.1.c
-- ext/minimap2/lib/simde/test/x86/sse4.2.c
-- ext/minimap2/lib/simde/test/x86/ssse3.c
-- ext/minimap2/lib/simde/test/x86/svml.c
-- ext/minimap2/lib/simde/test/x86/test-avx.h
-- ext/minimap2/lib/simde/test/x86/test-avx512.h
-- ext/minimap2/lib/simde/test/x86/test-mmx.h
-- ext/minimap2/lib/simde/test/x86/test-sse.h
-- ext/minimap2/lib/simde/test/x86/test-sse2.h
-- ext/minimap2/lib/simde/test/x86/test-x86-internal.h
-- ext/minimap2/lib/simde/test/x86/test-x86.c
-- ext/minimap2/lib/simde/test/x86/test-x86.h
 - ext/minimap2/main.c
 - ext/minimap2/map.c
 - ext/minimap2/minimap.h

data/ext/minimap2/lib/simde/CONTRIBUTING.md

@@ -1,114 +0,0 @@
-# Contributing to SIMDe
-
-First off, if you're even reading this, thank you!  There is a lot of
-work to do, and any help is appreciated.
-
-If you haven't already, please read the
-[README](https://github.com/nemequ/simde/blob/master/README.md).  The
-[wiki](https://github.com/nemequ/simde/wiki) also has some good
-information, especially the
-[FAQ](https://github.com/nemequ/simde/wiki/FAQ) and a guide on how to
-[implement a new
-function](https://github.com/nemequ/simde/wiki/Implementing-a-New-Function).
-
-For information on developing for architectures you don't have access
-to, please see the [Development
-Environment](https://github.com/nemequ/simde/wiki/Development-Environment)
-page on the wiki.
-
-If you still have questions, or if anything below doesn't make sense
-to you, please feel free to use the [issue
-tracker](https://github.com/nemequ/simde/issues) or the [mailing
-list](https://groups.google.com/forum/#!forum/simde) to ask.  I know
-the SIMDe documentation needs a lot of improvement, and asking
-questions will help us understand what is missing, so please don't be
-shy!
-
-## Building the Tests
-
-SIMDe contains an extensive test suite used for development.  Most
-users will never need to build the suite, but if you're contributing
-code to SIMDe you'll need to build them.
-
-Here is the basic procedure for compiling the tests:
-
-```bash
-mkdir test/build
-cd test/build
-CFLAGS="-march=native" CXXFLAGS="-march=native" cmake ..
-make -j
-./run-tests
-```
-
-Note that `-march=native` may not be the right flag for your compiler.
-That should work for most compilers on x86/x86_64, though MSVC is an
-exception (try `/arch:AVX2` instead of `-march=native`).  On other
-architectures please consult your compiler documentation to find out
-what flags you should use to enable the SIMD extension for your target
-platform.  Here are a few to try:
-
- * ARM:
-   * `-march=armv8-a+simd` (for ARMv8)
-   * `-march=armv7-a -mfpu=neon` (for ARMv7)
- * POWER
-   * `-mcpu=native`
-
-If you need a flag not listed above, please let us know so we can add
-it to the list.
-
-## Coding Style
-
-SIMDe uses two spaces for indentation.  Please adjust your editor
-accordingly.
-
-The coding style for preprocessor macros is a bit mixed since I made
-some changes mid-project.  For new code, please indent the
-preprocessor conditions before the hash to the same level as the
-normal code would be, and indent the code inside of preprocessor
-conditions as if the conditions were normal code.  For example:
-
-```c
-int
-foo(void) {
-  #if 1
-    bar();
-  #else
-    baz();
-  #endif
-}
-```
-
-Other than that, please just try to follow the existing style.  We'll
-add new rules here as the need arises.
-
-## Commit Messages
-
-Git commit messages should contain lines no longer than 72 characters.
-The first line should always be a one-line summary of the commit, with
-the relevant component followed by a colon and a space (if
-applicable), then the summary.
-
-If the one-line summary is insufficient to fully describe the changes
-further descriptive paragraphs should be added, separated by blank
-lines.
-
-For example:
-
-```
-sse: add magical code to make everything go fast
-
-Lorem ipsum dolor sit amet, consectetur adipiscing elit. Curabitur
-interdum scelerisque risus non ultricies. Vivamus id tristique mauris.
-Mauris et augue vel urna aliquam posuere. Morbi in sem nec ante
-ullamcorper ultrices in quis nibh. In felis velit, semper a mauris sed,
-congue ullamcorper enim. Vestibulum ante ipsum primis in faucibus orci
-luctus et ultrices posuere cubilia Curae; Nulla facilisi. Donec
-scelerisque elit dui, et aliquet magna tincidunt eu.
-
-Curabitur rhoncus lacus ac elit pulvinar, quis posuere ante ultrices.
-Suspendisse at mauris vitae justo pretium tempor et in mauris. Nunc
-facilisis nulla a ante tincidunt, imperdiet rhoncus metus interdum.
-Vivamus sed nunc vel tellus porta consequat. Donec quis porttitor elit,
-et cursus urna. Donec et sapien lorem. In imperdiet magna at aliquet
-hendrerit.
-```

data/ext/minimap2/lib/simde/COPYING

@@ -1,20 +0,0 @@
-Copyright (c) 2017 Evan Nemerson <evan@nemerson.com>
-
-Permission is hereby granted, free of charge, to any person obtaining
-a copy of this software and associated documentation files (the
-"Software"), to deal in the Software without restriction, including
-without limitation the rights to use, copy, modify, merge, publish,
-distribute, sublicense, and/or sell copies of the Software, and to
-permit persons to whom the Software is furnished to do so, subject to
-the following conditions:
-
-The above copyright notice and this permission notice shall be
-included in all copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
-MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
-LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
-OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
-WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.