<commit_before>P = bwt_lcp
CC = gcc
CFLAGS = -std=c99 -Wall -Wno-char-subscripts -O3
LDFLAGS = -lz -lm

$(P): $(P).c $(P).h kseq.h dictionary.h dictionary.c streams.h streams.c algorithms.h algorithms.c
	$(CC) $(CFLAGS) $(P).c dictionary.c streams.c algorithms.c -o $(P) $(LDFLAGS) && mkdir -p tests/arrays tests/outputFiles tests/supportFiles tests/supportLists tests/BWT tests/LCP tests/supportBWT tests/supportLCP

clean:
	@echo "Cleaning..."
	rm -rf *.o *.out *.exe $(P) tests/arrays/* decode_bwt decode_lcp tests/arrays/* tests/outputFiles/* tests/supportFiles/* tests/supportLists/* tests/BWT/* tests/LCP/* tests/supportBWT/* tests/supportLCP/* tests/B_W_T

decode_bwt: util/decode_bwt.c
	$(CC) $(CFLAGS) util/decode_bwt.c -o decode_bwt $(LDFLAGS)

decode_lcp: util/decode_lcp.c
	$(CC) $(CFLAGS) util/decode_lcp.c -o decode_lcp $(LDFLAGS)	

test:
	./$(P) tests/uploaded_test.fasta<commit_msg>build all programs<commit_after>P = bwt_lcp
CC = gcc
CFLAGS = -std=c99 -Wall -Wno-char-subscripts -O3
LDFLAGS = -lz -lm

bin: $(P) decode_bwt decode_lcp

$(P): $(P).c $(P).h kseq.h dictionary.h dictionary.c streams.h streams.c algorithms.h algorithms.c
	$(CC) $(CFLAGS) $(P).c dictionary.c streams.c algorithms.c -o $(P) $(LDFLAGS) && mkdir -p tests/arrays tests/outputFiles tests/supportFiles tests/supportLists tests/BWT tests/LCP tests/supportBWT tests/supportLCP

clean:
	@echo "Cleaning..."
	rm -rf *.o *.out *.exe $(P) tests/arrays/* decode_bwt decode_lcp tests/arrays/* tests/outputFiles/* tests/supportFiles/* tests/supportLists/* tests/BWT/* tests/LCP/* tests/supportBWT/* tests/supportLCP/* tests/B_W_T

decode_bwt: util/decode_bwt.c
	$(CC) $(CFLAGS) util/decode_bwt.c -o decode_bwt $(LDFLAGS)

decode_lcp: util/decode_lcp.c
	$(CC) $(CFLAGS) util/decode_lcp.c -o decode_lcp $(LDFLAGS)	

test:
	./$(P) tests/uploaded_test.fasta
{'fraction_non_alphanumeric': 0.16466739367502725, 'fraction_numerical': 0.003271537622682661, 'mean_word_length': 4.334302325581396, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, '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': '4830945', 'n_tokens_mistral': 728, 'n_tokens_neox': 705, 'n_words': 167}