Get sample names from vcf.

vcf-samples.sh

#! /bin/env bash

function error() { >&2 echo -e "\033[31m$*\033[0m"; }
function stop() { error "$*"; exit 1; }
try() { "$@" || stop "cannot $*"; }

file=$1
#doesn't work for double extension .gvcf.gz
ext="${file##*.}"
search=

function usage {
echo "usage: $0 <file>"
}

if [[ "$ext" == "gvcf" || "$ext" == "vcf" ]]
then
    search=grep
elif [[ "$ext" == "gz" ]]
then
    search=zgrep
else
    usage
    stop "unrecognised extension $ext"
fi


$search -m1 '^#CHROM' $file | tr '\t' '\n' | grep -v -F -f <(echo '#CHROM,POS,ID,REF,ALT,QUAL,FILTER,INFO,FORMAT' | tr ',' '\n')