diff --git a/Makefile b/Makefile index a5b1806..8408523 100644 --- a/Makefile +++ b/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 ; +## Vasimuddin Md ; Sanchit Misra ; +## Chirag Jain ; Heng Li +## */ +## 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) diff --git a/build_rmi.sh b/build_rmi.sh index d162799..627567e 100755 --- a/build_rmi.sh +++ b/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 diff --git a/index.c b/index.c index cd78061..b629066 100644 --- a/index.c +++ b/index.c @@ -167,7 +167,7 @@ void mm_idx_dump_hash(const char* f_name, const mm_idx_t *mi) std::map> 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;