ruby-minigraph 0.0.20.0

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data/LICENSE.txt

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+The MIT License (MIT)
+
+Copyright (c) 2020 kojix2
+
+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.

data/README.md

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+# ruby-minigraph
+
+[![Gem Version](https://badge.fury.io/rb/ruby-minigraph.svg)](https://badge.fury.io/rb/ruby-minigraph)
+[![test](https://github.com/kojix2/ruby-minigraph/actions/workflows/ci.yml/badge.svg)](https://github.com/kojix2/ruby-minigraph/actions/workflows/ci.yml)
+[![Docs Latest](https://img.shields.io/badge/docs-latest-blue.svg)](https://kojix2.github.io/ruby-minigraph/)
+[![The MIT License](https://img.shields.io/badge/license-MIT-blue.svg)](LICENSE.txt)
+[![DOI](https://zenodo.org/badge/339645970.svg)](https://zenodo.org/badge/latestdoi/339645970)
+
+:curly_loop: [minigraph](https://github.com/lh3/minigraph) - the sequence-to-graph mapper - for [Ruby](https://github.com/ruby/ruby)
+
+:construction: under development
+
+## Installation
+
+You need to install it from the source code. Because you need to build minigraph and create a shared library. Open your terminal and type the following commands in order. 
+
+```sh
+git clone --recursive https://github.com/kojix2/ruby-minigraph
+cd ruby-minigraph
+bundle install
+bundle exec rake minigraph:build
+bundle exec rake install
+```
+
+You can run tests to see if the installation was successful. 
+
+```
+bundle exec rake test
+```
+
+## Quick Start
+
+```ruby
+require "minigraph"
+```
+
+## APIs
+
+## Development
+
+```sh
+git clone --recursive https://github.com/kojix2/ruby-minigraph
+# git clone https://github.com/kojix2/ruby-minigraph
+# cd ruby-minigraph
+# git submodule update -i
+cd ruby-minigraph
+bundle install
+bundle exec rake minigraph:build
+bundle exec rake test
+```
+
+## Contributing
+
+ruby-minigraph is a library under development and there are many points to be improved. 
+If you improve the source code, please feel free to send us your pull request. 
+Typo corrections are also welcome. 
+
+Bug reports and pull requests are welcome on GitHub at https://github.com/kojix2/ruby-minigraph.
+
+## License
+
+[MIT License](https://opensource.org/licenses/MIT).

data/ext/Rakefile

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+# frozen_string_literal: true
+
+require "rake"
+require "fileutils"
+require "ffi"
+
+minigraph_dir = File.expand_path("minigraph", __dir__)
+target_dir = "../../vendor"
+target_fname = FFI.map_library_name("minigraph")
+target_path = File.join(target_dir, target_fname)
+
+task default: ["minigraph:build", "minigraph:clean"]
+
+namespace :minigraph do
+  desc "Compile Minigraph"
+  task :build do
+    Dir.chdir(minigraph_dir) do
+      # Add -fPIC option to Makefile
+      sh "git apply ../minigraph.patch"
+      sh "cp ../cmappy/cmappy.h ../cmappy/cmappy.c ."
+      # case RbConfig::CONFIG["host_cpu"]
+      sh "make"
+      # end
+      case RbConfig::CONFIG["host_os"]
+      when /mswin|msys|mingw|cygwin|bccwin|wince|emc/
+        warn "windows not supported"
+        sh "cc *.o -shared -o #{target_fname} -lm -lz -lpthread"
+      when /darwin|mac os/
+        sh "clang -dynamiclib -undefined dynamic_lookup -o #{target_fname} *.o -lm -lz -lpthread"
+        sh "otool -L #{target_fname}"
+      else
+        sh "cc *.o -shared -o #{target_fname} -lm -lz -lpthread"
+        sh "ldd -r #{target_fname}"
+      end
+      sh "rm cmappy.h cmappy.c"
+      sh "git apply -R ../minigraph.patch"
+      FileUtils.mkdir_p(target_dir)
+      warn "mkdir -p #{target_dir}"
+      sh "mv #{target_fname} #{target_path}"
+    end
+  end
+
+  desc "make clean"
+  task :clean do
+    Dir.chdir(minigraph_dir) do
+      sh "make clean"
+    end
+  end
+
+  desc "`make clean` and remove shared lib"
+  task cleanall: [:clean] do
+    Dir.chdir(minigraph_dir) do
+      sh "rm #{target_path}" if File.exist?(target_path)
+    end
+  end
+end

data/ext/cmappy/cmappy.c

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+#include "cmappy.h"
+
+int mg_verbose_level(int v)
+{
+	if (v >= 0) mg_verbose = v;
+	return mg_verbose;
+}

data/ext/cmappy/cmappy.h

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+#ifndef CMAPPY_H
+#define CMAPPY_H
+
+#include "minigraph.h"
+
+int mg_verbose_level(int v);
+
+#endif

data/ext/minigraph/LICENSE.txt

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+The MIT License
+
+Copyright (c) 2019-     Dana-Farber Cancer Institute
+
+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.

data/ext/minigraph/Makefile

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+CC=			gcc
+CFLAGS=		-g -Wall -Wc++-compat -std=c99 -msse4 -O3
+CPPFLAGS=
+INCLUDES=
+OBJS=		kalloc.o kthread.o algo.o sys.o gfa-base.o gfa-io.o gfa-aug.o gfa-bbl.o gfa-ed.o \
+            sketch.o misc.o bseq.o options.o shortk.o miniwfa.o \
+			index.o lchain.o gchain1.o galign.o gcmisc.o map-algo.o cal_cov.o \
+			format.o gmap.o ggsimple.o ggen.o asm-call.o
+PROG=		minigraph
+LIBS=		-lz -lpthread -lm
+
+ifneq ($(asan),)
+	CFLAGS+=-fsanitize=address
+	LIBS+=-fsanitize=address -ldl
+endif
+
+.SUFFIXES:.c .o
+.PHONY:all clean depend
+
+.c.o:
+		$(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@
+
+all:$(PROG)
+
+minigraph:$(OBJS) main.o
+		$(CC) $(CFLAGS) $^ -o $@ $(LIBS)
+
+clean:
+		rm -fr gmon.out *.o a.out $(PROG) *~ *.a *.dSYM
+
+depend:
+		(LC_ALL=C; export LC_ALL; makedepend -Y -- $(CFLAGS) $(DFLAGS) -- *.c)
+
+# DO NOT DELETE
+
+algo.o: kalloc.h algo.h miniwfa.h kvec-km.h ksort.h
+asm-call.o: mgpriv.h minigraph.h gfa.h ggen.h bseq.h gfa-priv.h algo.h
+bseq.o: bseq.h kvec-km.h kalloc.h kseq.h
+cal_cov.o: mgpriv.h minigraph.h gfa.h gfa-priv.h algo.h kalloc.h
+format.o: kalloc.h mgpriv.h minigraph.h gfa.h
+galign.o: mgpriv.h minigraph.h gfa.h kalloc.h miniwfa.h
+gchain1.o: mgpriv.h minigraph.h gfa.h ksort.h khashl.h kalloc.h gfa-priv.h
+gcmisc.o: mgpriv.h minigraph.h gfa.h kalloc.h
+gfa-aug.o: gfa-priv.h gfa.h ksort.h
+gfa-base.o: gfa-priv.h gfa.h kstring.h khashl.h kalloc.h ksort.h
+gfa-bbl.o: gfa-priv.h gfa.h kalloc.h ksort.h kvec.h
+gfa-ed.o: gfa-priv.h gfa.h kalloc.h ksort.h khashl.h kdq.h kvec-km.h
+gfa-io.o: kstring.h gfa-priv.h gfa.h kseq.h
+ggen.o: kthread.h kalloc.h sys.h bseq.h ggen.h minigraph.h gfa.h mgpriv.h
+ggen.o: gfa-priv.h
+ggsimple.o: mgpriv.h minigraph.h gfa.h gfa-priv.h kalloc.h bseq.h algo.h
+ggsimple.o: sys.h ggen.h kvec-km.h
+gmap.o: kthread.h kalloc.h bseq.h sys.h mgpriv.h minigraph.h gfa.h gfa-priv.h
+index.o: mgpriv.h minigraph.h gfa.h khashl.h kalloc.h kthread.h kvec-km.h
+index.o: sys.h
+kalloc.o: kalloc.h
+kthread.o: kthread.h
+lchain.o: mgpriv.h minigraph.h gfa.h kalloc.h krmq.h
+main.o: mgpriv.h minigraph.h gfa.h gfa-priv.h sys.h ketopt.h
+map-algo.o: kalloc.h mgpriv.h minigraph.h gfa.h khashl.h ksort.h
+miniwfa.o: miniwfa.h kalloc.h
+misc.o: mgpriv.h minigraph.h gfa.h ksort.h
+options.o: mgpriv.h minigraph.h gfa.h sys.h
+shortk.o: mgpriv.h minigraph.h gfa.h ksort.h kavl.h algo.h khashl.h kalloc.h
+sketch.o: kvec-km.h kalloc.h mgpriv.h minigraph.h gfa.h
+sys.o: sys.h

data/ext/minigraph/NEWS.md

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+Release 0.20-r559 (20 November 2022)
+------------------------------------
+
+This release fixes several assertion failures (#78, #79 and #80) caused by
+recent changes in graph chaining. It also fixes an integer overflow that may
+happen to chromosomes longer than 256 Mb (#76). Results remain the same.
+
+(20 November 2022, r559)
+
+
+
+Release 0.19-r551 (12 June 2022)
+--------------------------------
+
+This release fixes a segmental fault if minigraph is compiled with certain
+compiler-libc combinations. This is apparently caused by memcpy(0,0,0).
+Minigraph is otherwise identical v0.18.
+
+(12 June 2022, r551)
+
+
+
+Release 0.18-r538 (9 May 2022)
+------------------------------
+
+This release uses heuristics to speed up base alignment in long divergent
+regions. The heuristics does not guarantee optimal alignment but it reliably
+produces alignment close to the optimal except in centromeres where the
+algorithmically optimal alignment may not represent true evolution in biology.
+The new version is 10-700% faster than v0.17 depending on input data and
+parameters in use.
+
+(9 May 2022, r538)
+
+
+
+Release 0.17-r524 (29 April 2022)
+---------------------------------
+
+This release adds base alignment to minigraph. It represents the first major
+improvement to minigraph. Specifically, this release attempts to connect linear
+chains with the graph wavefront alignemnt algorithm (GWFA) and produces the
+final alignment with miniwfa under the 2-piece gap penalty. Graph generation
+also considers base alignment. This gives more accurate graph alignment and
+generally simpler graph topology. Note that minigraph still focuses on
+structural variations and does not generate base-level graphs. To endusers,
+minigraph remains similar feature wise.
+
+Notable changes:
+
+ * New feature: option `-c` for base alignment and graph generation. In the
+   alignment mode, the option adds the `cg:Z` CIGAR tag like minimap2. Graph
+   generation still works without `-c` but applying this option is generally
+   recommended now.
+
+It should be noted that the base alignment is currently slow for species of
+high diversity. This will be addressed in the next couple of releases.
+
+(29 April 2022, r524)
+
+
+
+Release 0.16-r436 (21 February 2022)
+------------------------------------
+
+Notable changes:
+
+ * Improvement: 2-level chaining. This is a feature backported from minimap2.
+   It speeds up graph generation for human graphs.
+
+ * Improvement: break a chain at poorly aligned regions, another recent
+   minimap2 feature.
+
+ * Added the script for generating figures in the minigraph paper.
+
+(21 February 2022, r436)
+
+
+
+Release 0.15-r426 (21 March 2021)
+---------------------------------
+
+Fixed a bug in bubble identification around inversions. This version should be
+used together with the latest gfatools for consistency.
+
+(21 March 2021, r426)
+
+
+
+Release 0.14-r415 (19 December 2020)
+------------------------------------
+
+Notable changes:
+
+ * Added the `--call` option to find the allele/walk in each bubble.
+
+ * Reduced the default minimum variant length (option `-L`) from 100 to 50 for
+   the consistency with the SV community.
+
+(19 December 2020, r415)
+
+
+
+Release 0.13-r397 (3 December 2020)
+-----------------------------------
+
+Notable change:
+
+ * Fixed incorrect anchors in linear chains. In older versions, a linear chain
+   may contain two anchors with identical reference or query coordinates.
+
+(3 December 2020, r397)
+
+
+
+Release 0.12-r389 (26 October 2020)
+-----------------------------------
+
+Notable changes:
+
+ * Improve alignments towards ends of graph segments. If there is an SV close to
+   the ends but not at the ends, older versions may produce an excessively
+   large bubble including high-identity matches.
+
+ * Heuristically accelerates alignment in complex subgraphs by skipping
+   many unnecessary sequence-aware graph traversals. This speeds up graph
+   generation for CHM13 by three folds without obviously affecting accuracy.
+
+ * Added option --inv to optionally disable inversions. Graph traversal is hard
+   with inversions.
+
+ * Fixed the bug that prevents large -K.
+
+ * Apply option -K4g to the asm preset.
+
+ * Added option --write-mz to output the positions of minimizer anchors.
+
+(26 October 2020, r389)
+
+
+
+Release 0.11-r371 (13 September 2020)
+-------------------------------------
+
+Notable changes:
+
+ * Added option --max-rmq-size to limit the max RMQ size, which is set 100k by
+   default. This heuristic reduces the long running time for aligning long
+   centromeric sequences. The accuracy might be affected in rare cases.
+
+ * Cap the max k-mer occurrence to 250 by default. For maize genomes, the
+   current heuristic may choose an occurrence cutoff larger than 1000. This
+   makes minigraph too slow to be practical.
+
+ * Added option -S to output more detailed information about linear chains.
+
+ * Added option -D to ignore diagonal minimizer anchors. This is useful to
+   mapping a sequence against itself.
+
+(13 September 2020, r371)
+
+
+
+Release 0.10-r356 (14 February 2020)
+------------------------------------
+
+Notable changes:
+
+ * Older releases miss a small fraction of INDELs involving repeats. This
+   release fixes this issue.
+
+ * Added the "stableGaf" command to mgutils.js to convert unstable GAF (e.g. by
+   GraphAligner) to stable GAF.
+
+(14 February 2020, r356)
+
+
+
+Release 0.9-r343 (31 December 2019)
+-----------------------------------
+
+Notable changes:
+
+ * RMQ based linear chaining. The chaining accuracy should be higher for large
+   events. The speed remains similar.
+
+ * Use ksw2 to check the sequence divergence of events to be inserted.
+
+ * Treat inversions as special events. Don't insert them as long substitutions.
+
+(31 December 2019, r343)
+
+
+
+Release 0.8-r316 (11 December 2019)
+-----------------------------------
+
+This release reduces suboptimal chains caused by the chaining heuristics. It
+generates slightly simpler human graphs.
+
+(11 December 2019, r316)
+
+
+
+Release 0.7-r310 (21 November 2019)
+-----------------------------------
+
+Notable changes:
+
+ * Increased the default maximum INDEL/event length from 10kb to 100kb for
+   assembly mapping and graph generation.
+
+ * Decreased the default minimum INDEL/event length from 250bp to 100bp.
+
+ * Accelerated graph mapping by pre-filtering isolated anchors and disconnected
+   linear chains. This triples the performance when long gaps are desired.
+
+Due to the change of default parameters, this release generates graphs
+different from the previous versions.
+
+(21 November 2019, r310)
+
+
+
+Release 0.6-r302 (17 November 2019)
+-----------------------------------
+
+Notable changes:
+
+ * Assign weight to seeds based on their repetitiveness. This helps chaining in
+   repetitive regions a little bit.
+
+ * For short-read mapping, prefer the reference path if the alternate path is
+   not much better.
+
+Major changes may be coming in the next release.
+
+(17 November 2019, r302)
+
+
+
+Release 0.5-r285 (8 September 2019)
+-----------------------------------
+
+Notable changes:
+
+ * Fixed a bug that leads to wrong mapping positions in GAF.
+
+ * Fixed two bugs related to graph chaining.
+
+ * Added option `-j` to set expected sequence divergence and to adjust other
+   chaining parameters accordingly.
+
+ * Increased the k-mer thresholds for fast divergence estimate. This improves
+   the alignment around low-complexity regions.
+
+ * Tuned the default parameters to add highly divergent events only.
+
+ * Warn about duplicated sequence names in graph construction (#3).
+
+This version generates graphs different from the previous versions. The mapping
+accuracy is improved due to the bug fixes and parameter tuning.
+
+(8 September 2019, r285)
+
+
+
+Release 0.4-r267 (22 August 2019)
+---------------------------------
+
+Notable changes:
+
+ * Support paired-end mapping for short reads.
+
+ * Remap and calculate coverage (see the new --cov option in the manpage).
+
+ * Fixed multiple edges in the generated graphs. The v0.3 14-genome graph
+   contains one multiple edge.
+
+ * Use dynamic minimizer occurrence cutoff. For human data, the dynamic cutoff
+   is around 137, higher than the default cutoff 100 used in earlier versions.
+   As a result, graph generations will become a little slower.
+
+Due to the last two changes, graphs generated with this version are different
+from the previous versions.
+
+(22 August 2019, r267)
+
+
+
+Release 0.3-r243 (7 August 2019)
+--------------------------------
+
+This release generates graphs with SR tags on L-lines. The topology of the
+graph is identical to the one generated with v0.2.
+
+(7 August 2019, r243)
+
+
+
+Release 0.2-r235 (19 July 2019)
+-------------------------------
+
+This release fixes multiple minor bugs. It also considers k-mer matches and
+improves the accuracy of graph chaining. Nonetheless, the old chaining
+algorithm, albeit simple, works quite well. The improvement is marginal.
+
+(19 July 2019, r235)
+
+
+
+Release 0.1-r191 (6 July 2019)
+------------------------------
+
+Initial proof-of-concept release.
+
+(6 July 2019, r191)