<commit_before>#!/bin/bash -l
#SBATCH
#SBATCH --nodes=1
#SBATCH --mem=110G
#SBATCH --partition=parallel
#SBATCH --time=12:00:00

NM=final
SAMP=ERR194147
NTHREADS=24
MEM="100G"

if [ ! -f "${SAMP}.sam/${NM}.bam" ] ; then
    sambamba view -S -f bam "${SAMP}.sam/${NM}.sam" > "${SAMP}.sam/${NM}.bam"
fi
if [ ! -f "${SAMP}.sam/${NM}.sorted.bam" ] ; then
    mkdir -p "sambamba_temp_${SAMP}"
    sambamba sort --tmpdir="sambamba_temp_${SAMP}" -p -m ${MEM} -t ${NTHREADS} "${SAMP}.sam/${NM}.bam" "${SAMP}.sam/${NM}.sorted.bam"
fi
<commit_msg>sort input bam<commit_after>#!/bin/bash -l
#SBATCH
#SBATCH --nodes=1
#SBATCH --mem=110G
#SBATCH --partition=parallel
#SBATCH --time=4:00:00

SAMP=ERR194147
NTHREADS=24
MEM="100G"

for NM in input final ; do
    if [ ! -f "${SAMP}.sam/${NM}.bam" ] ; then
	sambamba view -S -f bam "${SAMP}.sam/${NM}.sam" > "${SAMP}.sam/${NM}.bam"
    fi
    if [ ! -f "${SAMP}.sam/${NM}.sorted.bam" ] ; then
	TEMP="sambamba_temp_${SAMP}_${NM}"
	mkdir -p "${TEMP}"
	sambamba sort --tmpdir="${TEMP}" -p -m ${MEM} -t ${NTHREADS} "${SAMP}.sam/${NM}.bam" "${SAMP}.sam/${NM}.sorted.bam"
    fi
done


{'fraction_non_alphanumeric': 0.25426774483378256, 'fraction_numerical': 0.036837376460017966, 'mean_word_length': 3.680672268907563, 'pattern_counts': {'":': 0, '<': 3, '<?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': '655379', 'n_tokens_mistral': 505, 'n_tokens_neox': 505, 'n_words': 99}