<commit_before># art_illumina [options] -i <DNA_reference_file> -l <read_length> -f <fold_coverage> -o <outFile_prefix>
#
# Relevant options:
#  -mp  --matepair indicate a mate-pair read simulation
#  -p   --paired   indicate a paired-end read simulation
#       NOTE: art will automatically switch to a mate-pair read simulation if the given mean fragment size >= 2000
#  -l   --len      the length of reads to be simulated
#  -f   --fcov     the fold of read coverage to be simulated
#  -m   --mflen    the mean size of DNA fragments for paired-end simulations
#  -s   --sdev     the standard deviation of DNA fragment size for paired-end simulations.
#  -na  --noALN    do not output ALN alignment file
#  -rs  --rndSend  the seed for random number generator (default: system time in second)

# Use wgsim to generate unpaired Illumina-like reads.  Macro takes
# parameters: (1) batch name, (2) reference genome, (3) read length in
# batch, (4) # reads in batch, (5) pseudo-random seed.
define art_ill_unp_reads

# Generate unpaired reads
r0_art_$1.fq.gz: $$(FA) $$(QSIM_EXPERIMENTS_HOME)/software/art/art_illumina
	$$(QSIM_EXPERIMENTS_HOME)/software/art/art_illumina -sam -na -rs $5 -l $3 -f $4 -i $2 -o .$$@
	python $(QSIM_EXPERIMENTS_HOME)/bin/art_convert.py --in1 .$$(@).fq --sam .$$(@).sam --out1 .$$(@).final.fq
	rm -f .$$(@).fq .$$(@).sam
	gzip -c .$$(@).final.fq > $$@
	rm -f .$$(@).final.fq
	$$(QSIM_EXPERIMENTS_HOME)/software/art/art_illumina 2>&1 > $$@.version

endef

# Use wgsim to generate paired-end Illumina-like reads.  Macro takes
# parameters: (1) batch name, (2) reference genome, (3) read length in
# batch, (4) average fold-coverage, (5) mean fragment length, (6)
# stddev for fragment length, (7) pseudo-random seed.
define art_ill_pair_reads

# Generate paired-end reads
r1_art_$1.fq.gz: $(FA) $$(FA) $$(QSIM_EXPERIMENTS_HOME)/software/art/art_illumina
	$$(QSIM_EXPERIMENTS_HOME)/software/art/art_illumina -sam -na -p -rs $7 -m $5 -s $6 -l $3 -f $4 -i $2 -o .$$@
	python $(QSIM_EXPERIMENTS_HOME)/bin/art_convert.py --in1 .$$(@)1.fq --in2 .$$(@)2.fq --sam .$$(@).sam --out1 .$$(@).final1.fq --out2 .$$(@).final2.fq
	rm -f .$$(@)1.fq .$$(@)2.fq .$$(@).sam
	gzip -c .$$(@).final1.fq > $$@
	gzip -c .$$(@).final2.fq > $$(@:r1_%=r2_%)
	rm -f .$$(@).final1.fq .$$(@).final2.fq
	$$(QSIM_EXPERIMENTS_HOME)/software/art/art_illumina 2>&1 > $$@.version

endef
<commit_msg>fixing typos in art sim file<commit_after># art_illumina [options] -i <DNA_reference_file> -l <read_length> -f <fold_coverage> -o <outFile_prefix>
#
# Relevant options:
#  -i   --in       the filename of input DNA/RNA reference
#  -mp  --matepair indicate a mate-pair read simulation
#  -p   --paired   indicate a paired-end read simulation
#       NOTE: art will automatically switch to a mate-pair read simulation if the given mean fragment size >= 2000
#  -l   --len      the length of reads to be simulated
#  -f   --fcov     the fold of read coverage to be simulated
#  -m   --mflen    the mean size of DNA fragments for paired-end simulations
#  -s   --sdev     the standard deviation of DNA fragment size for paired-end simulations.
#  -na  --noALN    do not output ALN alignment file
#  -rs  --rndSend  the seed for random number generator (default: system time in second)

# Use art to generate unpaired Illumina-like reads.  Macro takes
# parameters: (1) batch name, (2) reference genome, (3) read length in
# batch, (4) # reads in batch, (5) pseudo-random seed.
define art_ill_unp_reads

# Generate unpaired reads
r0_art_$1.fq.gz: $$(FA) $$(QSIM_EXPERIMENTS_HOME)/software/art/art_illumina
	$$(QSIM_EXPERIMENTS_HOME)/software/art/art_illumina -sam -na -rs $5 -l $3 -f $4 -i $2 -o .$$@
	python $(QSIM_EXPERIMENTS_HOME)/bin/art_convert.py --in1 .$$(@).fq --sam .$$(@).sam --out1 .$$(@).final.fq
	rm -f .$$(@).fq .$$(@).sam
	gzip -c .$$(@).final.fq > $$@
	rm -f .$$(@).final.fq
	$$(QSIM_EXPERIMENTS_HOME)/software/art/art_illumina 2>&1 > $$@.version

endef

# Use art to generate paired-end Illumina-like reads.  Macro takes
# parameters: (1) batch name, (2) reference genome, (3) read length in
# batch, (4) average fold-coverage, (5) mean fragment length, (6)
# stddev for fragment length, (7) pseudo-random seed.
define art_ill_pair_reads

# Generate paired-end reads
r1_art_$1.fq.gz: $(FA) $$(FA) $$(QSIM_EXPERIMENTS_HOME)/software/art/art_illumina
	$$(QSIM_EXPERIMENTS_HOME)/software/art/art_illumina -sam -na -p -rs $7 -m $5 -s $6 -l $3 -f $4 -i $2 -o .$$@
	python $(QSIM_EXPERIMENTS_HOME)/bin/art_convert.py --in1 .$$(@)1.fq --in2 .$$(@)2.fq --sam .$$(@).sam --out1 .$$(@).final1.fq --out2 .$$(@).final2.fq
	rm -f .$$(@)1.fq .$$(@)2.fq .$$(@).sam
	gzip -c .$$(@).final1.fq > $$@
	gzip -c .$$(@).final2.fq > $$(@:r1_%=r2_%)
	rm -f .$$(@).final1.fq .$$(@).final2.fq
	$$(QSIM_EXPERIMENTS_HOME)/software/art/art_illumina 2>&1 > $$@.version

endef

{'fraction_non_alphanumeric': 0.1776723070573669, 'fraction_numerical': 0.021460998761865455, 'mean_word_length': 3.4063636363636363, 'pattern_counts': {'":': 0, '<': 11, '<?xml version=': 0, '>': 27, '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': '5774722', 'n_tokens_mistral': 1986, 'n_tokens_neox': 1820, 'n_words': 555}