<commit_before>#!/usr/bin/env bash

# This shebang make the code more portable.
# Sometimes you don't know where bash, perl or python is...

set -e

# Recommended to work with regex
shopt -s extglob

# Maybe the code is being called from a symbolic link (e.g. bin folder insted of src)
abspath_script="$(readlink -f -e "$0")"
script_absdir="$(dirname "$abspath_script")"
script_name="$(basename "$0")"

#============== pathway based on the system ==================
# picard samtofastq.jar file path
#SAMTOFASTQ="/v4scratch/lp364/SamToFastq.jar"
SAMTOFASTQ="$script_absdir/SamToFastq.jar"
<commit_msg>Update - Bowtie: added quality score, mismatches, distance between reads and multiple alignment constraints. - Added stdout state update: total # of reads and percentages after each step. - Realistic example: containing sequences from chrM and rRNA with a mismatch in one of the reads.<commit_after>#!/usr/bin/env bash

set -e
shopt -s extglob # Recommended to work with regex

abspath_script="$(readlink -f -e "$0")"
script_absdir="$(dirname "$abspath_script")"
script_name="$(basename "$0")"

#============== pathway based on the system ==================
# picard samtofastq.jar file path
#SAMTOFASTQ="/v4scratch/lp364/SamToFastq.jar"
SAMTOFASTQ="$script_absdir/SamToFastq.jar"

{'fraction_non_alphanumeric': 0.15834633385335414, 'fraction_numerical': 0.0093603744149766, 'mean_word_length': 5.447236180904523, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, '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': '3919411', 'n_tokens_mistral': 438, 'n_tokens_neox': 401, 'n_words': 135}