When I run bam-readcount with a site-list file containing only one line, a start..stop span of 21 bases, it produces the expected output, with one record for each of the 21 bases, and the record for the midpoint base has a status string for the bases "-AA" (among others), which is what I expect. If I run it instead with a site-list file containing that SAME exact span AND many others on other lines of the file, none of which overlap that span, it again produces (among the output) one record for each of the 21 bases, but the record for the midpoint base DOES NOT include a status for bases -AA.
Why would this happen? The same bam file and same reference file are used in each case. Why wouldn't it be repeatable?
I do not know what version of bam-readcount I'm running; I can't find a way to get it to report the version number. I believe it is vintage 2014 though.