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make multi

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Saurabh
2021-06-16 00:39:09 -07:00
committed by Heng Li
parent 0369874d4e
commit b2ff8fbe92
3 changed files with 44 additions and 2 deletions
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42
Makefile
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@@ -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)

2
build_rmi.sh
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@@ -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

2
index.c
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@@ -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;