porting from old sambamba/BioD

[RichardCorbett]

Hi folks,

I have some old D code that I can't compile anymore and I want to port it to use newer versions.

In my code I have some use of the read object that no longer is supported. For example,

//aligned, not chastity failed, not supp, not secondary - add to X calcs
if(!read.is_duplicate || read.is_duplicate && dupsInX) {
  xCalcSum+=read.sequence_length;
  xCalcSumAlnOnly+=read.basesQueried;
}

when trying to compile using the more recent version of BioD I get the following

 Error: no property 'basesQueried' for type 'BamRead'

I can't seem to find any docs describing what basesQueried this might be called in more recent versions. I'm looking for the length of the aligned parts of the read. Do you have any ideas?

thanks RIchard

[pjotrp]

I don't think it is part of sambamba.