<commit_before>#!/bin/sh

WASP_VER=0.2.1
WASP_DIR="../../software/wasp/WASP-${WASP_VER}"
FIND_SNPS="python ${WASP_DIR}/mapping/find_intersecting_snps.py"

if [ "$1" = "scavenger" ] ; then
PART1="#SBATCH --partition=scavenger"
PART2="#SBATCH --qos=scavenger"
else
PART1="#SBATCH --partition=shared"
PART2=""
fi

for dat in ERR050082_1 ERR050083_1 ; do
for pe in unp pair ; do
for ext in bwa bt2 snap ; do

cat >.${dat}.${ext}.${pe}.wasp.sh <<EOF
#!/bin/sh

#SBATCH
#SBATCH --job-name=Wasp
#SBATCH --nodes=1
${PART1}
${PART2}
#SBATCH --time=8:00:00
#SBATCH --mem=4G

mkdir -p ${dat}.${ext}.${pe}.sorted.bam.out
$FIND_SNPS --is_sorted --output_dir ${dat}.${ext}.${pe}.sorted.bam.out --snp_dir snps ../real_data/${dat}.${ext}.${pe}.sorted.bam
EOF
echo "sbatch .${dat}.${ext}.${pe}.wasp.sh"

done
done
done
<commit_msg>use latest cloned version of WASP<commit_after>#!/bin/sh

WASP_DIR="../../software/wasp/wasp-github"
FIND_SNPS="python ${WASP_DIR}/mapping/find_intersecting_snps.py"

if [ "$1" = "scavenger" ] ; then
PART1="#SBATCH --partition=scavenger"
PART2="#SBATCH --qos=scavenger"
else
PART1="#SBATCH --partition=shared"
PART2=""
fi

for dat in ERR050082_1 ERR050083_1 ; do
for pe in unp pair ; do
for ext in bwa bt2 snap ; do

cat >.${dat}.${ext}.${pe}.wasp.sh <<EOF
#!/bin/sh

#SBATCH
#SBATCH --job-name=Wasp
#SBATCH --nodes=1
${PART1}
${PART2}
#SBATCH --time=8:00:00
#SBATCH --mem=4G

mkdir -p ${dat}.${ext}.${pe}.sorted.bam.out
$FIND_SNPS --is_sorted --output_dir ${dat}.${ext}.${pe}.sorted.bam.out --snp_dir snps ../real_data/${dat}.${ext}.${pe}.sorted.bam
EOF
echo "sbatch .${dat}.${ext}.${pe}.wasp.sh"

done
done
done

{'fraction_non_alphanumeric': 0.22481572481572482, 'fraction_numerical': 0.03746928746928747, 'mean_word_length': 4.340983606557377, 'pattern_counts': {'":': 0, '<': 7, '<?xml version=': 0, '>': 5, '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': '7126287', 'n_tokens_mistral': 751, 'n_tokens_neox': 717, 'n_words': 142}