make gen_coverage_file accept compressed files

[Sanrrone]

Dears,
along with greeting you, the gen_coverage_file script to generate the coverages only accept .fastq sequences, but my files (which are more than 2000) are all compressed. in fq.gz format, How can make the script accept the compressed format?

thanks in advance!

[ziyewang]

Hi,

Is the sequencing data pair-end, single-end or interleaved? If it's pair-end, the original code can be used directly by just modifying the input options. If not, I'll update the code to support compressed files.

"Options:
-f Forward read suffix for paired reads (default="_1.fastq")
-r Reverse read suffix for paired reads (default="_2.fastq")"

Best,
Ziye

[Sanrrone]

Hi,
They are single end compressed. But I could do a workaround by using the same command inside the script (bwa + samtools).

thank you!