From ba186a4c780118d5394223a8e53b19ea5271f7b9 Mon Sep 17 00:00:00 2001 From: Saurabh Date: Thu, 18 Nov 2021 22:32:05 -0800 Subject: [PATCH] TAL submodule --- .gitmodules | 3 +++ Makefile | 1 + ext/TAL | 1 + lchain.c | 3 ++- 4 files changed, 7 insertions(+), 1 deletion(-) create mode 160000 ext/TAL diff --git a/.gitmodules b/.gitmodules index a80f848..ab9bf2b 100644 --- a/.gitmodules +++ b/.gitmodules @@ -1,3 +1,6 @@ [submodule "lib/simde"] path = lib/simde url = https://github.com/nemequ/simde.git +[submodule "ext/TAL"] + path = ext/TAL + url = https://github.com/IntelLabs/Trans-Omics-Acceleration-Library.git diff --git a/Makefile b/Makefile index 1d0fc3f..90f19de 100644 --- a/Makefile +++ b/Makefile @@ -37,6 +37,7 @@ endif #INCLUDES= #INCLUDES= -I./ext/TAL_offline/src/LISA-hash #-I./ext/TAL/src/dynamic-programming +INCLUDES= -I./ext/TAL/src/LISA-hash -I./ext/TAL/src/dynamic-programming OBJS= kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o \ lchain.o align.o hit.o seed.o map.o format.o pe.o esterr.o splitidx.o \ ksw2_ll_sse.o diff --git a/ext/TAL b/ext/TAL new file mode 160000 index 0000000..2a97815 --- /dev/null +++ b/ext/TAL @@ -0,0 +1 @@ +Subproject commit 2a97815a5fcf80b611134ed0a9d89d2bd0fcbdec diff --git a/lchain.c b/lchain.c index febd636..23521a8 100644 --- a/lchain.c +++ b/lchain.c @@ -6,7 +6,8 @@ #include "kalloc.h" #include "krmq.h" //#include "simd_chain.h" -#include "parallel_chaining_32_bit.h" +//#include "parallel_chaining_32_bit.h" +#include "parallel_chaining_v2_22.h" extern uint64_t dp_time, rmq_time, rmq_t1, rmq_t2, rmq_t3, rmq_t4;