compare reads ignoring read id

[statgen]

compare reads ignoring read id

[mktrost]

Sorry, for the delayed response. I just got back from vacation traveling overseas. Yes, that is the correct place to make the modification. But in the code you included above you are only checking that the flags are the same. I think you also want to add a check for the same sequence.

Then depending on what you want in your output, you may want to update the getDiffs/writeDiffDiffs/writeBamDiffs methods to check for readName differences.

Let me know if you have any additional questions.
Mary Kate