Samtools Flagstats - library HtsJDK

Question

[guipagui]

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

[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.

[Pierre Lindenbaum]

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

which one ?

[guipagui]

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

Answer 1

[Pierre Lindenbaum]

• 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.