make multi

Makefile

@@ -1,3 +1,34 @@
+
+## /* The MIT License
+## 
+## Copyright (c) 2018-     Dana-Farber Cancer Institute
+##               2017-2018 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.
+## Modified Copyright (C) 2021 Intel Corporation
+##    Contacts: Saurabh Kalikar <saurabh.kalikar@intel.com>; 
+## 	Vasimuddin Md <vasimuddin.md@intel.com>; Sanchit Misra <sanchit.misra@intel.com>; 
+## 	Chirag Jain <chirag@iisc.ac.in>; Heng Li <hli@jimmy.harvard.edu>
+## */
+## 
 CFLAGS=		-Wall -O2 -Wc++-compat #-Wextra
 CPPFLAGS=	-DHAVE_KALLOC -march=native
 
@@ -84,6 +115,17 @@ libminimap2.a:$(OBJS)
 sdust:sdust.c kalloc.o kalloc.h kdq.h kvec.h kseq.h ketopt.h sdust.h
 		$(CC) -D_SDUST_MAIN $(CFLAGS) $< kalloc.o -o $@ -lz
 
+multi:
+		$(MAKE) clean
+		$(MAKE)
+		mv minimap2 mm2-fast
+		$(MAKE) clean
+		$(MAKE) lhash=1
+		mv minimap2 mm2-fast-lhash
+		$(MAKE) clean
+		$(MAKE) no_opt=1
+		mv minimap2 mm2-fast-no-opt
+
 # SSE-specific targets on x86/x86_64
 
 ifeq ($(arm_neon),)   # if arm_neon is defined, compile this target with the default setting (i.e. no -msse2)

build_rmi.sh

@@ -12,6 +12,6 @@ full_path=`readlink -f $kv_file`
 
 cd ./ext/TAL
 make lisa_hash
-./build-lisa-hash-index $kv_file
+./build-lisa-hash-index $full_path
 
 rm ../../temp_read.fastq

index.c

@@ -167,7 +167,7 @@ void mm_idx_dump_hash(const char* f_name, const mm_idx_t *mi)
 	std::map<uint64_t, vector<uint64_t>> m;
 
 	ofstream f(f_name);
-	fprintf(stderr, "Building sorted key-val map");
+	fprintf(stderr, "Building sorted key-val map\n");
 
 	uint32_t i,j;
 	uint64_t num_values = 0;