search

amplab / snap

Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data
https://www.microsoft.com/en-us/research/project/snap/
Apache License 2.0
287 stars 66 forks source link

what is the command looks like for SNAP paired to use stdin/stdout #85

Closed wangzhenkeep closed 7 years ago

wangzhenkeep commented 7 years ago

The sinlge command looks like : snap single myIndex -fastq - -o -sam -. Dose pairend support to use stdin/stdout? And can you give an example?

Thanks!

bolosky commented 7 years ago

The issue with paired reads is that you’ve only got one stdin for two files.

If you have an interleaved FASTQ (read pairs that come one after another, so four lines for the first end then four lines for the second, repeated) then you can do it (BTW, this is not a standard file format, we made it up). As you can with SAM or BAM input. Or you could take one end from stdin and one from an input file, although it’s kind of hard to imagine how that would come up.

So:

snap paired myIndex -pairedInterleavedFastq - -o -sam – snap paired myIndex -pairedFastq – secondEndFile.fq -o -sam – snap paired myIndex -sam - -o -sam –

I’m not sure what else we can do given the limitations of how input redirection works.

--Bill

From: CelLoud王震 [mailto:notifications@github.com] Sent: Sunday, March 5, 2017 6:11 PM To: amplab/snap snap@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [amplab/snap] what is the command looks like for SNAP paired to use stdin/stdout (#85)

The sinlge command looks like : snap single myIndex -fastq - -o -sam -. Dose pairend support to use stdin/stdout? And can you give an example?

Thanks!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Famplab%2Fsnap%2Fissues%2F85&data=02%7C01%7Cbolosky%40microsoft.com%7C5615856f8642408d235f08d46436061e%7C72f988bf86f141af91ab2d7cd011db47%7C1%7C0%7C636243630577769283&sdata=UTr0vX5fbnNby5t%2F3SxsLPL6gYmw8hJjoqR7AB%2B0hlo%3D&reserved=0, or mute the threadhttps://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAA752UHUbtmPB3-oXgogpTZWXB2Mnk8lks5ri2sugaJpZM4MTpvY&data=02%7C01%7Cbolosky%40microsoft.com%7C5615856f8642408d235f08d46436061e%7C72f988bf86f141af91ab2d7cd011db47%7C1%7C0%7C636243630577769283&sdata=6JYYLxvc6pKc8RZjVomu%2Fd7E6djFnyH9SL97e3flM0g%3D&reserved=0.

wangzhenkeep commented 7 years ago

Thanks！！！！
“snap paired myIndex -sam - -o -sam –” ，I like this command very much.