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Bam Viewer That Works On Authenticated Ftp Urls With Username/Password Combination?

Are there any BAM file viewers that will work on authenticated ftp urls with username/password combination?

For example, something like this:

~/myfavouritebamviewer view ftp://username:password@my.ftp.site/file.bam
next-gen bam software
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updated by Istvan Albert Istvan Albert • written by Biostar User • Biostar User

you could try to mount this site as a directory with FUSE, then any viewer will treat files within as normal files

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written by Jeremy Leipzig Jeremy Leipzig

1 answer

Integrative Genomics Viewer (IGV) works with http sites that require authorization, I think it will work with FTP, a quick test indicates that it can connect, and most network libraries can handle http as well as ftp. That being said the FTP protocol is a lot trickier than HTTP as it has multiple modes of operation: active/passive plus other things. So this will also depend on the server settings.

(You may need to specify the username and/or password in the url, ouch!)

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written by Istvan Albert Istvan Albert

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