add gzip/xz/bzip2 support for input

[sharkLoc]

• Support for reading gzip, xz, and bzip2 compressed files
• Combine the magic numbers and file extensions of the files to determine the compression type. Any condition that is true can be used to determine the file type
• run chopper without any args will report Error: stdin not detected and exit

[JMencius]

@wdecoster I tested the performance of this pull version against the last version I submitted also using DM.fastq.gz. The performance is comparable, differences within 3 seconds.

[sharkLoc]

@JMencius ，Yes, this version only adds support for two additional compressed files (xz and bzip2), and fixes the problem that data will be lost when there are multiple members of GZ files

[sharkLoc]

Hi @wdecoster, i did a test
step1:

build multiple members gz file ,testGC.fastq in test-data dir

gzip -c testGC.fastq testGC.fastq > mutl.fq.gz

step2:
run command
chopper -i mutl.fq.gz --mingc 0.5

output :

result in chopper 0.8.0: Kept 6 reads out of 11 reads

in this pr version: Kept 12 reads out of 22 reads

[wdecoster]

run chopper without any args will report Error: stdin not detected and exit

Do you mean this was an error that is now fixed? It still works on stdin, right?

[sharkLoc]

yes, still work in stdin

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---- Replied Message ---- | From | Wouter De ***@***.***> | | Date | 05/21/2024 17:45 | | To | ***@***.***> | | Cc | Tao ***@***.***>***@***.***> | | Subject | Re: [wdecoster/chopper] add gzip/xz/bzip2 support for input (PR #34) | run chopper without any args will report Error: stdin not detected and exit Do you mean this was an error that is now fixed? It still works on stdin, right? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***>

[wdecoster]

Awesome!