<commit_before># Makefile for htslib, a C library for high-throughput sequencing data formats.
#
#    Copyright (C) 2013-2014 Genome Research Ltd.
#
#    Author: <NAME> <<EMAIL>>

CC     = gcc
AR     = ar
RANLIB = ranlib

# TODO: edit cram code to remove need for -DSAMTOOLS
CPPFLAGS = -I. -DSAMTOOLS=1
# TODO: probably update cram code to make it compile cleanly with -Wc++-compat
CFLAGS   = -g -Wall -O2
EXTRA_CFLAGS_PIC = -fpic
LDFLAGS  =
LDLIBS   =

prefix      = /usr/local
exec_prefix = $(prefix)
bindir      = $(exec_prefix)/bin
includedir  = $(prefix)/include
libdir      = $(exec_prefix)/lib
mandir      = $(prefix)/share/man
man1dir     = $(mandir)/man1
man5dir     = $(mandir)/man5

INSTALL = install -p
INSTALL_PROGRAM = $(INSTALL)
INSTALL_DATA    = $(INSTALL) -m 644

BUILT_PROGRAMS = \
	bgzip \
	tabix

BUILT_TEST_PROGRAMS = \
	test/fieldarith \<commit_msg>htslib allows user-defined CC, CFLAGS and CPPFLAGS<commit_after># Makefile for htslib, a C library for high-throughput sequencing data formats.
#
#    Copyright (C) 2013-2014 Genome Research Ltd.
#
#    Author: <NAME> <<EMAIL>>

CC     ?= gcc
AR     = ar
RANLIB = ranlib

# TODO: edit cram code to remove need for -DSAMTOOLS
CPPFLAGS += -I. -DSAMTOOLS=1
# TODO: probably update cram code to make it compile cleanly with -Wc++-compat
CFLAGS   := -g -Wall -O2 $(CFLAGS)
EXTRA_CFLAGS_PIC = -fpic
LDFLAGS  =
LDLIBS   =

prefix      = /usr/local
exec_prefix = $(prefix)
bindir      = $(exec_prefix)/bin
includedir  = $(prefix)/include
libdir      = $(exec_prefix)/lib
mandir      = $(prefix)/share/man
man1dir     = $(mandir)/man1
man5dir     = $(mandir)/man5

INSTALL = install -p
INSTALL_PROGRAM = $(INSTALL)
INSTALL_DATA    = $(INSTALL) -m 644

BUILT_PROGRAMS = \
	bgzip \
	tabix

BUILT_TEST_PROGRAMS = \
	test/fieldarith \
{'fraction_non_alphanumeric': 0.11941964285714286, 'fraction_numerical': 0.018973214285714284, 'mean_word_length': 3.199063231850117, 'pattern_counts': {'":': 0, '<': 9, '<?xml version=': 0, '>': 9, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '4475122', 'n_tokens_mistral': 700, 'n_tokens_neox': 654, 'n_words': 185}