Reverts loeblab/Duplex-Sequencing#32. There's still an issue with a failure to write any duplexes to file with this commit. I'm fairly sure this has to do with the firstTag=firstRead.qname.split(":")[0] line. I think the issue is that there are two duplex consensuses for each tag (one from each end of the insert). By not distinguishing between the two, the information associated with the tag overwrites the information associated with the other end of the insert in readDict, if it already exists, which means that a duplex can never be formed. I suspect your suspicion that there's a bug there is correct, but I'm not entirely sure exactly what it is. If you can break the other changes into smaller patches, I can merge those separately from this change.
Reverts loeblab/Duplex-Sequencing#32. There's still an issue with a failure to write any duplexes to file with this commit. I'm fairly sure this has to do with the firstTag=firstRead.qname.split(":")[0] line. I think the issue is that there are two duplex consensuses for each tag (one from each end of the insert). By not distinguishing between the two, the information associated with the tag overwrites the information associated with the other end of the insert in readDict, if it already exists, which means that a duplex can never be formed. I suspect your suspicion that there's a bug there is correct, but I'm not entirely sure exactly what it is. If you can break the other changes into smaller patches, I can merge those separately from this change.