<commit_before>#!/usr/bin/env bash
#BSUB -J gc_correct[1-300]%5
#BSUB -o logs/gc_correction.out
#BSUB -e logs/gc_correction.err
#BSUB -R "select[mem>10] rusage[mem=10]"
#BSUB -P Sikela

# catch unset variables, non-zero exits in pipes and calls, enable x-trace.
set -o nounset -o pipefail -o errexit -x

source code/1000genomes/config.sh

# LSB_JOBINDEX is the job array position
sample=${SAMPLES[$(($LSB_JOBINDEX - 1))]}

bed_file=$bed_dir/${sample}_read_depth.bed
gc_model=data/hg38_duf_full_domains_v2.2_GC.txt

Rscript code/gc_correction_test.R $sample $gc_model


<commit_msg>fix typo in 1000genomes batch GC correction script<commit_after>#!/usr/bin/env bash
#BSUB -J gc_correct[1-300]%5
#BSUB -o logs/gc_correction.out
#BSUB -e logs/gc_correction.err
#BSUB -R "select[mem>10] rusage[mem=10]"
#BSUB -P Sikela

# catch unset variables, non-zero exits in pipes and calls, enable x-trace.
set -o nounset -o pipefail -o errexit -x

source code/1000genomes/config.sh

# LSB_JOBINDEX is the job array position
sample=${SAMPLES[$(($LSB_JOBINDEX - 1))]}

bed_file=$bed_dir/${sample}_read_depth.bed
gc_model=data/hg38_duf_full_domains_v2.2_GC.txt

Rscript code/gc_correction.R $sample $gc_model



{'fraction_non_alphanumeric': 0.1273031825795645, 'fraction_numerical': 0.03350083752093802, 'mean_word_length': 5.096938775510204, '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': '239225', 'n_tokens_mistral': 519, 'n_tokens_neox': 485, 'n_words': 113}