The level attribute of the pysam.PileupRead class

[yorjo]

Hi,

What is the purpose of the level attribute in the PileupRead class?
The only documentation I can find on this is in the bam.h header of
samtools which says very little information:

@discussion See also bam_plbuf_push() and bam_lplbuf_push(). The
difference between the two functions is that the former does not
set bam_pileup1_t::level, while the later does. Level helps the
implementation of alignment viewers, but calculating this has some
overhead.

I tought that the level(Y-position) of each PileupRead would be pre-
calculated to prevent collision between reads. I wrote some code to
verify the PileupRead.level value and I don't understand the value
return by the module. Is it fully implemented and working?

Regards,

[Andreas]

Hi,

as far is I understand the level attribute gives the vertical (row)
placement
of a read in an alignment viewer to avoid reads overlapping in the
same row. Unless you want to write one, you can ignore this attribute.

Best wishes,
Andreas