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view bin/fastq-interleave @ 0:06f8460885ff

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migrate from GitHub
author yutaka-saito
date Sun, 19 Apr 2015 20:51:13 +0900
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#! /bin/bash

# Reads 2 fastq files, and writes them interleaved.
# Assumes 1 fastq per 4 lines, i.e. no line wrapping.

paste <(cat "$1" | paste - - - -) <(cat "$2" | paste - - - -) | tr '\t' '\n'

# Is this better?
#paste <(zcat -f "$1"|paste - - - -) <(zcat -f "$2"|paste - - - -)|tr '\t' '\n'

# This does not interpret "-" as stdin:
#paste <(paste - - - - < "$1") <(paste - - - - < "$2") | tr '\t' '\n'