#!/bin/bash set -e PE=testdata/four_reads.pe.fastq; R1=testdata/R1.fastq R2=testdata/R2.fastq interleaved=$(cat $R1 $R2 | ./target/debug/fasten_shuffle) shouldbe=$(cat $PE) if [ "$interleaved" != "$shouldbe" ]; then echo "ERROR: did not get interleaved reads" exit 1 fi tmpdir=$(mktemp --directory --tmpdir=. FRIENDS_JOEY.XXXXXX) trap " { rm -rf $tmpdir; } " EXIT # deshuffling test shouldbe_R1="$tmpdir/R1.fastq" shouldbe_R2="$tmpdir/R2.fastq" cat $PE | ./target/debug/fasten_shuffle --deshuffle -1 $shouldbe_R1 -2 $shouldbe_R2 if [ "$(cat $shouldbe_R1)" != "$(cat $R1)" ]; then echo "ERROR: did not deshuffle correctly to R1 (and probably to R2)" exit 1 fi if [ "$(cat $shouldbe_R2)" != "$(cat $R2)" ]; then echo "ERROR: did not deshuffle correctly to R2 but somehow made R1 correctly" exit 1 fi echo "$0 passed!"