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I have a bash script that I need to run for a series of files. The script takes 4 arguments. The first ref is a file, fun is a directory, R1arr and R2arr each are arrays containing a series of files with specific features in a given directory.

My script.sh is as follows:

ref="$1"
fun=$2
R1arr="$@"
R2arr="$@"

analyseReads -i "$ref" -o "$fun" --left "${R1arr[@]}" --right "${R2arr[@]}"

And I run it for various files as follows:

FORWARD=($(for i in Sample_STE*/*R1; do echo $i; done))
REVERSE=($(for i in Sample_STE*/*R2; do echo $i; done))

bash script.sh "$ref" "$fun" "${FORWARD[@]}" "${REVERSE[@]}"

I get an error since "${FORWARD[@]}" and "${REVERSE[@]}" does not only contain the files in the array FORWARD and REVERSE but it also contains "$ref" and "$fun". Why does this happen and how could I solve this issue?

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    At the operating-system level, an argument list on UNIX is a single array of NUL-delimited C strings. When you expand an array, each string it contains becomes a separate argument; the callee has no way of knowing where each individual array began and ended. Commented Oct 15, 2019 at 21:05
  • 1
    ...that said, the way you're assigning your arrays is buggy in the first place. It'd need to be FORWARD=( Sample_STE*/*R1 ) to not mangle the lists before you even try to do anything else with them. Commented Oct 15, 2019 at 21:06
  • 1
    R1arr="$@" is inherently buggy too; when you assign an array to a string variable, information about where the original boundaries were is lost. Commented Oct 15, 2019 at 21:08
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    BashPitfalls #50 is useful background on the side issue mentioned in my second comment. And BashPitfalls #14 explains a separate reason why the original code is broken. Commented Oct 15, 2019 at 21:09
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    The first of the two approaches given in my answer on the linked duplicate stackoverflow.com/questions/34905635/… will work for you; the second (pass-by-reference) one only works when calling shell functions, not calling external scripts. Commented Oct 15, 2019 at 21:12
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