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Samtools Flagstats - library HtsJDK

Hi,

I find which class run the command "Flagstats" with Samtools if i use the library Htsjdk, but i don't find it. It's possible? What is the name of the class?

Thanks a lot

software-error
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updated by Ram Ram • written by guipagui • guipagui

In Htsjdk, there is a class that run "idxstat" of samtools. I'll run "flagstats" as an external program with my java project, thanks a lot.

• 1 views • link
written by guipagui • guipagui

In Htsjdk, there is a class that run "idxstat" of samtools.

which one ?

• 1 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

I'm confuse, you have right, it's picard do it.

• 1 views • link
written by guipagui • guipagui

1 answer

  • samtools is a tool using the htslib C library
  • htsjdk is a only java library
  • as far as I know there is no java equivalent of the tool flagstats. You' ll have to write it.
• 1 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

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