minimap2 incorporated

.gitignore

@@ -6,8 +6,7 @@
 bin/abruijn-assemble
 bin/abruijn-polish
 bin/abruijn-repeat
+bin/abruijn-minimap2
 bin/blasr
 build
-lib/lemon-1.3.1/build
-lib/lemon-1.3.1/install
 lib/blasr_install/*

Makefile

@@ -1,21 +1,32 @@
-export COMMON = -I$(shell pwd)/src/include
-export LIBCUCKOO = -I$(shell pwd)/lib/libcuckoo
-export INTERVAL_TREE = -I$(shell pwd)/lib/interval_tree
-export LEMON = -I$(shell pwd)/lib/lemon
-export BIN_DIR = $(shell pwd)/bin
+ROOT_DIR := $(shell dirname $(realpath $(lastword $(MAKEFILE_LIST))))
+
+export COMMON = -I${ROOT_DIR}/src/include
+export LIBCUCKOO = -I${ROOT_DIR}/lib/libcuckoo
+export INTERVAL_TREE = -I${ROOT_DIR}/lib/interval_tree
+export LEMON = -I${ROOT_DIR}/lib/lemon
+export BIN_DIR = ${ROOT_DIR}/bin
+export MINIMAP2_DIR = ${ROOT_DIR}/lib/minimap2
 
 export CXXFLAGS = ${LIBCUCKOO} ${INTERVAL_TREE} ${LEMON} ${COMMON} 
 #export LDFLAGS = 
 
-.PHONY: clean all profile debug
+.PHONY: clean all profile debug minimap2
 
 .DEFAULT_GOAL := all
 
-all: 
+
+${BIN_DIR}/abruijn-minimap2:
+	make -C ${MINIMAP2_DIR}
+	cp ${MINIMAP2_DIR}/minimap2 ${BIN_DIR}/abruijn-minimap2
+
+minimap2: ${BIN_DIR}/abruijn-minimap2
+
+all: minimap2
 	make release -C src
-profile:
+profile: minimap2
 	make profile -C src
-debug:
+debug: minimap2
 	make debug -C src
-clean: 
+clean:
 	make clean -C src
+	make clean -C ${MINIMAP2_DIR}

README.md

@@ -14,9 +14,9 @@ step, which improves the structural accuracy of the resulting sequence.
 The algorithm also produces a graph representation of the final assembly.
 
 ABruijn has moderate memory requirements and is designed to run on a single node.
-Typically, assembly of a bacteria with 50x coverage takes less than half an hour 
-on a modern desktop and yeast assembly takes about 2 hours. A metagenome of total size 200 Mbp
-can be assembled within a day on using 70Gb of memory and 20 CPUs.
+Typically, assembly of a bacteria or yeast assembly takes less than half an hour 
+on a modern desktop. A whole human genome with 30x coverage could be assembled 
+within a week on a node with 32 CPUs and 800Gb RAM.
 
 Install
 -------
@@ -41,7 +41,7 @@ ABruijn package includes some third-party software:
 * libcuckoo [http://github.com/efficient/libcuckoo]
 * intervaltree [https://github.com/ekg/intervaltree]
 * lemon [http://lemon.cs.elte.hu/trac/lemon]
-* BLASR [https://github.com/PacificBiosciences/blasr]
+* minimap2 [https://github.com/lh3/minimap2]
 
 
 License

abruijn/alignment.py

@@ -21,7 +21,7 @@
 
 
 logger = logging.getLogger()
-MINIMAP_BIN = "minimap2"
+MINIMAP_BIN = "abruijn-minimap2"
 
 Alignment = namedtuple("Alignment", ["qry_id", "trg_id", "qry_start", "qry_end",
                                      "qry_sign", "qry_len", "trg_start",

docs/INSTALL.md

@@ -14,14 +14,7 @@ Requirements
 * GNU make
 * Python 2.7
 * Git
-* BLASR aligner [https://github.com/PacificBiosciences/blasr]
-
-
-BLASR installation
-------------------
-
-You can use 'install\_blasr.py' script for a local BLASR installation. You may skip
-this step if BLASR is already installed in your system.
+* Basic OS development headers (zlib, etc.)
 
 
 ABruijn Installation
@@ -42,5 +35,4 @@ Additonally, you may install the package for the better OS integration:
     python setup.py install
 
 Alternatively, you can perform local user installation by adding '--user' or '--prefix'
-options to the previous command. The system installation does not include BLASR, which 
-should be installed separately.
+options to the previous command.

docs/USAGE.md

@@ -221,7 +221,7 @@ as follows:
 Finally, ABruijn performs polishing of the resulting assembly
 to correct the remaining errors:
 
-* Alignment of all reads to the current assembly using BLASR
+* Alignment of all reads to the current assembly using minimap2
 * Selection of solid regions
 * Partition the total alignment of all reads into mini-alignments (bubbles)
 * Error correction of each bubble using a maximum likelihood approach

lib/minimap2/.gitignore

@@ -0,0 +1,8 @@
+.cproject
+.project
+.*.swp
+*.a
+*.o
+*.dSYM
+minimap2
+mappy.c

lib/minimap2/.travis.yml

@@ -0,0 +1,24 @@
+matrix:
+  include:
+    - language: c
+      compiler: gcc
+      script: make
+    - language: c
+      compiler: clang
+      script: make
+    - language: python
+      python: "2.7"
+      before_install: pip install cython
+      script: python setup.py build_ext
+    - language: python
+      python: "3.3"
+      before_install: pip install cython
+      script: python setup.py build_ext
+    - language: python
+      python: "3.5"
+      before_install: pip install cython
+      script: python setup.py build_ext
+    - language: python
+      python: "3.6"
+      before_install: pip install cython
+      script: python setup.py build_ext

lib/minimap2/LICENSE.txt

@@ -0,0 +1,23 @@
+The MIT License
+
+Copyright (c) 2017 Broad Institute, Inc.
+
+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.

lib/minimap2/MANIFEST.in

@@ -0,0 +1,11 @@
+include *.h
+include Makefile
+include ksw2_dispatch.c
+include getopt.c
+include main.c
+include README.md
+include python/mappy.c
+include python/cmappy.h
+include python/cmappy.pxd
+include python/mappy.pyx
+include python/README.rst

lib/minimap2/Makefile

@@ -0,0 +1,83 @@
+CFLAGS=		-g -Wall -O2 -Wc++-compat
+CPPFLAGS=	-DHAVE_KALLOC
+INCLUDES=
+OBJS=		kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o index.o chain.o align.o hit.o map.o format.o pe.o ksw2_ll_sse.o
+PROG=		minimap2
+PROG_EXTRA=	sdust minimap2-lite
+LIBS=		-lm -lz -lpthread
+
+ifeq ($(sse2only),)
+	OBJS+=ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o
+else
+	OBJS+=ksw2_extz2_sse.o ksw2_extd2_sse.o ksw2_exts2_sse.o
+endif
+
+.SUFFIXES:.c .o
+
+.c.o:
+		$(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@
+
+all:$(PROG)
+
+extra:all $(PROG_EXTRA)
+
+minimap2:main.o getopt.o libminimap2.a
+		$(CC) $(CFLAGS) main.o getopt.o -o $@ -L. -lminimap2 $(LIBS)
+
+minimap2-lite:example.o libminimap2.a
+		$(CC) $(CFLAGS) $< -o $@ -L. -lminimap2 $(LIBS)
+
+libminimap2.a:$(OBJS)
+		$(AR) -csru $@ $(OBJS)
+
+sdust:sdust.c getopt.o kalloc.o kalloc.h kdq.h kvec.h kseq.h sdust.h
+		$(CC) -D_SDUST_MAIN $(CFLAGS) $< getopt.o kalloc.o -o $@ -lz
+
+ksw2_extz2_sse41.o:ksw2_extz2_sse.c ksw2.h kalloc.h
+		$(CC) -c -msse4 $(CFLAGS) $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
+
+ksw2_extz2_sse2.o:ksw2_extz2_sse.c ksw2.h kalloc.h
+		$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY $(INCLUDES) $< -o $@
+
+ksw2_extd2_sse41.o:ksw2_extd2_sse.c ksw2.h kalloc.h
+		$(CC) -c -msse4 $(CFLAGS) $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
+
+ksw2_extd2_sse2.o:ksw2_extd2_sse.c ksw2.h kalloc.h
+		$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY $(INCLUDES) $< -o $@
+
+ksw2_exts2_sse41.o:ksw2_exts2_sse.c ksw2.h kalloc.h
+		$(CC) -c -msse4 $(CFLAGS) $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
+
+ksw2_exts2_sse2.o:ksw2_exts2_sse.c ksw2.h kalloc.h
+		$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY $(INCLUDES) $< -o $@
+
+ksw2_dispatch.o:ksw2_dispatch.c ksw2.h
+		$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
+
+clean:
+		rm -fr gmon.out *.o a.out $(PROG) $(PROG_EXTRA) *~ *.a *.dSYM build dist mappy.so mappy.c python/mappy.c mappy.egg*
+
+depend:
+		(LC_ALL=C; export LC_ALL; makedepend -Y -- $(CFLAGS) $(CPPFLAGS) -- *.c)
+
+# DO NOT DELETE
+
+align.o: minimap.h mmpriv.h bseq.h ksw2.h kalloc.h
+bseq.o: bseq.h kvec.h kalloc.h kseq.h
+chain.o: minimap.h mmpriv.h bseq.h kalloc.h
+example.o: minimap.h kseq.h
+format.o: kalloc.h mmpriv.h minimap.h bseq.h
+getopt.o: getopt.h
+hit.o: mmpriv.h minimap.h bseq.h kalloc.h khash.h
+index.o: kthread.h bseq.h minimap.h mmpriv.h kvec.h kalloc.h khash.h
+kalloc.o: kalloc.h
+ksw2_extd2_sse.o: ksw2.h kalloc.h
+ksw2_exts2_sse.o: ksw2.h kalloc.h
+ksw2_extz2_sse.o: ksw2.h kalloc.h
+ksw2_ll_sse.o: ksw2.h kalloc.h
+main.o: bseq.h minimap.h mmpriv.h getopt.h
+map.o: kthread.h kvec.h kalloc.h sdust.h mmpriv.h minimap.h bseq.h khash.h
+misc.o: minimap.h ksort.h
+pe.o: mmpriv.h minimap.h bseq.h kvec.h kalloc.h ksort.h
+sdust.o: kalloc.h kdq.h kvec.h sdust.h
+sketch.o: kvec.h kalloc.h minimap.h