Avoid expr substr in spades_compile.sh

[epruesse]

expr substr is not defined in posix and not implemented in MacOS /bin/expr. The much simpler bash substring expansion should be more widely compatible. It does work with MacOS' ancient /bin/bash.

[asl]

Great, thanks! Yes, spades_compile.sh is a bit complicated. Tagging @uncerso for review

[epruesse]

Great, thanks! Yes, spades_compile.sh is a bit complicated. Tagging @uncerso for review

For what it does, yes. Looks like someone had some fun with bash, but didn't know case/esac could do glob matching. Something like below would be easier to read. But then as long as the script works, it's all fine.

PASS_THROUGH_OPTS=()
while [[ $# -gt 0 ]]; do
  case $1 in
    -j|--threads)
      THREADS="$2"
      shift
      shift
   ;;
    *)
      PASS_THROUGH_OPTS+=("$1")
      shift
    ;;
  esac
done

Mostly I was just passing on patch from bioconda I had to add to get spades to even start compiling :)