bamutil diff - Get record for every read being compared

[DavidStreid]

Hi, I am wondering if I am using the tool correctly. Will there be a record for every QNAME in the bams being compared when comparing MAPQ scores? I am noticing my diff output includes only a fraction of the QNAME entries of one of my bams being diff'd.

$ bam diff --in1 ${BAM1} --in2 ${BAM2} --mapQual >> diffs.txt
$ cat diffs.txt | grep -v "<" | grep -v ">" | sort | uniq | wc -l.  # get only the read names, no diffs
7199
$ samtools view ${BAM1} | cut -f1 | sort | uniq | wc -l.            # qname/read names in my input bam
46367516

I am trying to determine whether one map/align method mapped reads with greater confidence than another. Thank you for any direction, correction, or help. Thanks!

[hyunminkang]

It will only report the differences. What was the exact issue here?

[DavidStreid]

Sorry for the delay - my issue was that I'm noticing that most reads weren't in the diff output and I was wondering why. That it only captures diffs, addresses that. Thank you. Related to this, is there any way to modify the options to compare all reads, even if they have been mapped to a different chromosome?