On Wed, Aug 6, 2014 at 2:19 PM, Wolfgang Maier <[email protected]> wrote: > 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):
You forgot the link to that discussion: https://groups.google.com/forum/#!topic/pysam-user-group/HTFch5Ejxd0 > 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 No, while SAM files ought to have @SQ lines they can often be missing (thus useful commands like samtools reheader exist), and if you had a SAM file of entirely unmapped reads there should be no @SQ lines at all. > - is this some kind of limitation of the samtools api or > - simply a bug in pysam Probably one of those - I'm not familiar enough with the samtools API to say which. Peter ------------------------------------------------------------------------------ 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
