bash template to reheader a VCF

reheader-vcf.sh

#!/bin/bash

set -eo pipefail

# http://stackoverflow.com/questions/9893667/is-there-a-way-to-write-a-bash-function-which-aborts-the-whole-execution-no-mat
trap "exit 1" TERM
export TOP_PID=$$

BGZIP=/gscmnt/gc2802/halllab/idas/software/local/bin/bgzip
TABIX=/gscmnt/gc2802/halllab/idas/software/local/bin/tabix
BCFTOOLS=/gscmnt/gc2802/halllab/idas/software/local/bin/bcftools1.4

function join_by { local IFS="$1"; shift; echo "$*"; }

function die {
    local timestamp=$(date +"%Y-%m-%d %T")
    echo "[ ${timestamp} ] ERROR: $@" >&2
    kill -s TERM ${TOP_PID}
}

function log {
    local timestamp=$(date +"%Y-%m-%d %T")
    echo "---> [ ${timestamp} ] $@" >&2
}

function run_cmd {
    local cmd=$1
    log "EXEC: ${cmd}"
    eval "${cmd}"
    if [[ $? -ne 0 ]]; then
        die "[err] Problem running command: ${cmd} !"
        exit 1;
    fi
}

function tabix_and_finalize_vcf {
    local tmpvcf=$1
    local finalvcf=$2
    local cmd="
    ${TABIX} -p vcf -f ${tmpvcf} \
        && mv ${tmpvcf}.tbi ${finalvcf}.tbi \
        && mv ${tmpvcf} ${finalvcf}
    "
    run_cmd "${cmd}"
}

function vcf_reheader {
    local header_vcf=$1
    local content_vcf=$2

    log "(vcf_reheader) calling bcftools subprocess"
    local cmd="
    cat <(${BCFTOOLS} view -h ${header_vcf} | head -n -1) \
        <(${BCFTOOLS} view -h ${content_vcf} | tail -n 1) \
        <(${BCFTOOLS} view -H ${content_vcf})
    "
    run_cmd "${cmd}"
}

function update_vcf {
    local header_vcf=$1
    local input_vcf=$2
    local output_vcf=$3

    if [[ -e "${output_vcf}" ]]; then
        log "shortcutting update_vcf"
        return 0;
    fi

    local tmpvcf=${output_vcf}.tmp

    local cmd1="
    vcf_reheader ${header_vcf} ${input_vcf} \
        | ${BGZIP} -c \
        > ${tmpvcf}
    "
    run_cmd "${cmd1}"
    tabix_and_finalize_vcf ${tmpvcf} ${output_vcf}
}

function main {
    local header_vcf=/gscmnt/gc2758/analysis/ccdg_gatk_callsets/t1d_2017.03.31/post-vqsr/7-vep-cadd-annotation/22:20000001-30000000/annotated.vep.cadd.c22:20000001-30000000.vcf.gz
    local input_vcf=$1
    local output_vcf=$2

    update_vcf $header_vcf $input_vcf $output_vcf
}

INPUT_VCF=$1
OUTPUT_VCF=$2

main $INPUT_VCF $OUTPUT_VCF ;