<commit_before>
# first 1Mbp of chr1
# 10000 SNPs (1%)
# 5000 indels (0.5%)
# 500 inversions of size 1-100bp (50 * 500 = 0.025%)

INPUT_SEQ=../chr21.1Mb.fa
STAMPY_HSH=../chr21
NINDIVS=1
PLOIDY=2
KMER=31
NSNPS=10000
NINDELS=5000
NINV=500
INVLEN=100
READLEN=100
MPSIZE=250
ALLELECOVG=30
ERROR=error
#error or noerror

all: $(INPUT_SEQ)
	../run-sample-pop.sh $(INPUT_SEQ) $(STAMPY_HSH) $(NINDIVS) $(PLOIDY) $(KMER) $(NSNPS) $(NINDELS) $(NINV) $(INVLEN) $(READLEN) $(MPSIZE) $(ALLELECOVG) $(ERROR) print > run.sh
	chmod +x run.sh
	./run.sh

clean:
	rm -rf genomes reads graphs bubbles vcfs gap_sizes* mp_sizes*

.PHONY: all clean<commit_msg>Added missing steps to test Makefile<commit_after>
# first 1Mbp of chr1
# 10000 SNPs (1%)
# 5000 indels (0.5%)
# 500 inversions of size 1-100bp (50 * 500 = 0.025%)

INPUT_SEQ=../chr21.1Mb.fa
STAMPY_HSH=../chr21
NINDIVS=1
PLOIDY=2
KMER=31
NSNPS=10000
NINDELS=5000
NINV=500
INVLEN=100
READLEN=100
MPSIZE=250
ALLELECOVG=30
ERROR=error
#error or noerror

all: ../chr21.1Mb.fa ../chr21.1Mb.fa.fai
	../run-sample-pop.sh $(INPUT_SEQ) $(STAMPY_HSH) $(NINDIVS) $(PLOIDY) $(KMER) $(NSNPS) $(NINDELS) $(NINV) $(INVLEN) $(READLEN) $(MPSIZE) $(ALLELECOVG) $(ERROR) print > run.sh
	chmod +x run.sh
	./run.sh

../chr21.1Mb.fa:
	gzip -c ../chr21.1Mb.fa.gz > ../chr21.1Mb.fa
../chr21.1Mb.fa.fai:
	samtools faidx ../chr21.1Mb.fa

clean:
	rm -rf genomes reads graphs bubbles vcfs gap_sizes* mp_sizes*

.PHONY: all clean
{'fraction_non_alphanumeric': 0.1732776617954071, 'fraction_numerical': 0.10090466249130133, 'mean_word_length': 4.2290909090909095, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 6, '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': '2213123', 'n_tokens_mistral': 795, 'n_tokens_neox': 673, 'n_words': 154}