Dear all, I've been asking this in the pysam user group, but didn't get any answers there, so I am giving it one more try here on this bigger list (it may well be a samtools api question anyway): pysam refuses to provide an iterator over reads in sam files that don't specify an @SQ sequence dictionary in their header (if you're asking for one, it raises - a somewhat misleading - "NotImplementedError: can not iterate over samfile without header"). There seems to be a good reason for this, since if you bypass the error, then sometimes (though, interestingly, not with every sam file) the Python interpreter crashes immediately when you try to retrieve the first read.
I am trying to understand what is going on here and why, so I guess my question is: - is an @SQ entry in the header an absolute technical requirement to retrieve reads from a samfile or - is this some kind of limitation of the samtools api or - simply a bug in pysam ? Thanks for any explanation, Wolfgang ------------------------------------------------------------------------------ Infragistics Professional Build stunning WinForms apps today! Reboot your WinForms applications with our WinForms controls. Build a bridge from your legacy apps to the future. http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
