<commit_before>#!/bin/bash
shift
FULL_READS_INPUT=$1
READS_FASTQ=$2
TEMP_FILENAME1=$3
OUTPUT=$4
JOB_DIR=$5
# Grab the variables and functions we need:
. ${JOB_DIR}/constants.sh
. ${JOB_DIR}/auto-options.sh

    RESOURCES_LAST_EXEC_PATH=${RESOURCES_ARTIFACTS_LAST_ARTIFACT_BINARIES}/bin/lastal
    RESOURCES_LAST_MERGE_BATCHES_EXEC=${RESOURCES_ARTIFACTS_LAST_ARTIFACT_BINARIES}/scripts/last-merge-batches.py
    RESOURCES_LAST_MAP_PROBS_EXEC=${RESOURCES_ARTIFACTS_LAST_ARTIFACT_BINARIES}/scripts/last-map-probs.py
    RESOURCES_LAST_BISULFITE_FORWARD_MATRIX=${RESOURCES_ARTIFACTS_LAST_ARTIFACT_BINARIES}/examples/bisulfite_f.mat
    RESOURCES_LAST_BISULFITE_REVERSE_MATRIX=${RESOURCES_ARTIFACTS_LAST_ARTIFACT_BINARIES}/examples/bisulfite_r.mat



    ORG=` echo ${ORGANISM} | tr [:lower:] [:upper:]  `
    BUILD_NUMBER=`echo ${GENOME_REFERENCE_ID} | awk -F\. '{print $1}' | tr [:lower:] [:upper:] `
    ENSEMBL_RELEASE=`echo ${GENOME_REFERENCE_ID} | awk -F\. '{print $(NF)}'| tr [:lower:] [:upper:] `

    INDEX_DIRECTORY=$(eval echo \${RESOURCES_ARTIFACTS_LAST_BISULFITE_INDEX_INDEX_${ORG}_${BUILD_NUMBER}_${ENSEMBL_RELEASE}}/)
    TOPLEVEL_DIRECTORY=$(eval echo \${RESOURCES_ARTIFACTS_LAST_BISULFITE_INDEX_TOPLEVEL_IDS_${ORG}_${BUILD_NUMBER}_${ENSEMBL_RELEASE}}/)
    REFERENCE=
    #make sure index exists
    if [ ! -e ${INDEX_DIRECTORY}/index_f.prj ]; then
        failThisLine
      	dieUponError "last-bisulfite index could not be found"<commit_msg>Remove script name's input argument from align-bisulfite-both-strands.sh only when needed.<commit_after>#!/bin/bash

[ $# -eq 6 ] && shift
FULL_READS_INPUT=$1
READS_FASTQ=$2
TEMP_FILENAME1=$3
OUTPUT=$4
JOB_DIR=$5
# Grab the variables and functions we need:
. ${JOB_DIR}/constants.sh
. ${JOB_DIR}/auto-options.sh

    RESOURCES_LAST_EXEC_PATH=${RESOURCES_ARTIFACTS_LAST_ARTIFACT_BINARIES}/bin/lastal
    RESOURCES_LAST_MERGE_BATCHES_EXEC=${RESOURCES_ARTIFACTS_LAST_ARTIFACT_BINARIES}/scripts/last-merge-batches.py
    RESOURCES_LAST_MAP_PROBS_EXEC=${RESOURCES_ARTIFACTS_LAST_ARTIFACT_BINARIES}/scripts/last-map-probs.py
    RESOURCES_LAST_BISULFITE_FORWARD_MATRIX=${RESOURCES_ARTIFACTS_LAST_ARTIFACT_BINARIES}/examples/bisulfite_f.mat
    RESOURCES_LAST_BISULFITE_REVERSE_MATRIX=${RESOURCES_ARTIFACTS_LAST_ARTIFACT_BINARIES}/examples/bisulfite_r.mat



    ORG=` echo ${ORGANISM} | tr [:lower:] [:upper:]  `
    BUILD_NUMBER=`echo ${GENOME_REFERENCE_ID} | awk -F\. '{print $1}' | tr [:lower:] [:upper:] `
    ENSEMBL_RELEASE=`echo ${GENOME_REFERENCE_ID} | awk -F\. '{print $(NF)}'| tr [:lower:] [:upper:] `

    INDEX_DIRECTORY=$(eval echo \${RESOURCES_ARTIFACTS_LAST_BISULFITE_INDEX_INDEX_${ORG}_${BUILD_NUMBER}_${ENSEMBL_RELEASE}}/)
    TOPLEVEL_DIRECTORY=$(eval echo \${RESOURCES_ARTIFACTS_LAST_BISULFITE_INDEX_TOPLEVEL_IDS_${ORG}_${BUILD_NUMBER}_${ENSEMBL_RELEASE}}/)
    REFERENCE=
    #make sure index exists
    if [ ! -e ${INDEX_DIRECTORY}/index_f.prj ]; then
        failThisLine
      	dieUponError "last-bisulfite index could not be found"
{'fraction_non_alphanumeric': 0.1281624500665779, 'fraction_numerical': 0.004993342210386152, 'mean_word_length': 6.311435523114355, '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': '3635850', 'n_tokens_mistral': 1321, 'n_tokens_neox': 1152, 'n_words': 146}