Program gto_fastq_pack

The gto_fastq_pack packages each FASTQ read in a single line. It can show the read score first or the dna sequence, depending on the execution mode.

For help type:


			  			./gto_fastq_pack -h

In the following subsections, we explain the input and output paramters.

Input parameters

The gto_fastq_pack program needs two streams for the computation, namely the input and output standard. The input stream is a FASTQ file.

The attribution is given according to:


			  			Usage: ./gto_fastq_pack [options] [[--] args]
or: ./gto_fastq_pack [options]

It packages each FASTQ read in a single line.

-h, --help            show this help message and exit

Basic options
< input.fastq         Input FASTQ file format (stdin)
> output.fastqpack    Output packaged FASTQ file format (stdout)

Optional
-s, --scores          When active, the application show the scores first

Example: ./gto_fastq_pack -s < input.fastq > output.fastqpack

An example of such an input file is:


			  			@SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=72
GNNTGATGGCCGCTGCCGATGGCGNANAATCCCACCAANATACCCTTAACAACTTAAGGGTTNTCAAATAGA
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IG9ICIIIIIIIIIIIIIIIIIIIIDIIIIIII>IIIIII/
@SRR001666.2 071112_SLXA-EAS1_s_7:5:1:801:338 length=72
NTTCAGGGATACGACGNTTGTATTTTAAGAATCTGNAGCAGAAGTCGATGATAATACGCGNCGTTTTATCAN
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII6IBIIIIIIIIIIIIIIIIIIIIIIIGII>IIIII-I)8I

Output

The output of the gto_fastq_pack program is a packaged FASTQ file.

Using the input above, an output example for this is the following:


			  			GNNTGATGGCCGCTGCCGATGGCGNANAATCCCACCAANATACCCTTAACAACTTAAGGGTTNTCAAATAGA
IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IG9ICIIIIIIIIIIIIIIIIIIIIDIIIIIII>IIIIII/
SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=72+	0
NTTCAGGGATACGACGNTTGTATTTTAAGAATCTGNAGCAGAAGTCGATGATAATACGCGNCGTTTTATCAN
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII6IBIIIIIIIIIIIIIIIIIIIIIIIGII>IIIII-I)8I
SRR001666.2 071112_SLXA-EAS1_s_7:5:1:801:338 length=72+	1

Another example for the same input, but using the scores first (flag ''s''), is:


			  			IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IG9ICIIIIIIIIIIIIIIIIIIIIDIIIIIII>IIIIII/
GNNTGATGGCCGCTGCCGATGGCGNANAATCCCACCAANATACCCTTAACAACTTAAGGGTTNTCAAATAGA
SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=72+	0
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII6IBIIIIIIIIIIIIIIIIIIIIIIIGII>IIIII-I)8I
NTTCAGGGATACGACGNTTGTATTTTAAGAATCTGNAGCAGAAGTCGATGATAATACGCGNCGTTTTATCAN
SRR001666.2 071112_SLXA-EAS1_s_7:5:1:801:338 length=72+	1