scanBam from Rsamtools is not importing one of my reads into R
Note the flag; that read is mapped in a reverse-complemented manner, so isMinusStrand = FALSE is filtering it out. I tested this by making a BAM file with only that read:

@SQ SN:I    LN:1000000
000000F|arrow   2064    I   336331  7   2926310H260M1774267H    *   00  *   *


Then in R:

&gt; library(Rsamtools)
&gt; blah = scanBam("foo.bam", param=ScanBamParam(what=scanBamWhat(), flag=scanBamFlag(isMinusStrand = TRUE)))[[1]]
&gt; blah$qname
[1] "000000F|arrow"
&gt; blah = scanBam("foo.bam", param=ScanBamParam(what=scanBamWhat(), flag=scanBamFlag(isMinusStrand = FALSE)))[[1]]
&gt; blah$qname
character(0)