<commit_before>#

# Sub directories containing source code, except for the main programs
SUBDIRS := include preqc-lr 

#
# Set libraries, paths, flags and options
#

#Basic flags every build needs
LIBS = -lz
CXXFLAGS ?= -g -O3
CXXFLAGS += -std=c++11
CFLAGS ?= -O3 -std=c99
CXX ?= g++
CC ?= gcc

# Include the src subdirectories
NP_INCLUDE=$(addprefix -I./, $(SUBDIRS))

# Add include flags
CPPFLAGS += $(NP_INCLUDE)

# Main programs to build
PROGRAM=preqclr

all: $(PROGRAM)

#
# Source files
#

# Find the source files by searching subdirectories<commit_msg>update makefile to include Heng Li's PAF parser, and seqtk lib<commit_after>#

# Sub directories containing source code, except for the main programs
SUBDIRS := include preqc-lr include/readpaf include/rapidjson/include include/zstr/src include/seqtk

#
# Set libraries, paths, flags and options
#

#Basic flags every build needs
LIBS = -lz -lboost_iostreams
CXXFLAGS ?= -g -O3
CXXFLAGS += -std=c++11 
CFLAGS ?= -O3 -std=c99
CXX ?= g++
CC ?= gcc

# Include the src subdirectories
NP_INCLUDE=$(addprefix -I./, $(SUBDIRS))

# Add include flags
CPPFLAGS += $(NP_INCLUDE)

# Main programs to build
PROGRAM=preqclr

all: $(PROGRAM)

#
# Source files
#

# Find the source files by searching subdirectories
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{'dir': 'git-commits-cleaned', 'id': '3759159', 'n_tokens_mistral': 461, 'n_tokens_neox': 428, 'n_words': 148}