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Update README.md
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sfchen authored Aug 6, 2018
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Expand Up @@ -100,7 +100,7 @@ repaq can read the input from STDIN, and write the output to STDOUT.

Here gives you an example of compressing the interleaved PE output from fastp by directly using pipes:
```shell
fastp -i R1.fq -I R2.fq --stdout | repaq --interleaved_in --stdin --stdout | xz > out.rpq.xz
fastp -i R1.fq -I R2.fq --stdout | repaq -c --interleaved_in --stdin --stdout | xz > out.rpq.xz
```

# FASTQ Format compatibility
Expand All @@ -119,7 +119,7 @@ options:
-o, --out1 output file name (string [=])
-I, --in2 read2 input file name when encoding paired-end FASTQ files (string [=])
-O, --out2 read2 output file name when decoding to paired-end FASTQ files (string [=])
-c, --compress compress input to output
-c, --compress compress input to output. This is the default mode
-d, --decompress decompress input to output
-k, --chunk the chunk size (kilo bases) for encoding, default 1000=1000kb. (int [=1000])
--stdin input from STDIN. If the STDIN is interleaved paired-end FASTQ, please also add --interleaved_in.
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