testing for NH tags presence
file has NH tags
examining read multiplicty
problem with region: chrIII-NC_003074 0 23459830 skipping
problem with region: chrII-NC_003071 0 19698289 skipping
problem with region: chrI-NC_003070 0 30427671 skipping
problem with region: chrIV-NC_003075 0 18585056 skipping
problem with region: chrV-NC_003076 0 26975502 skipping
Unique:	3211625
Unique Splices:	0
Multi:	0
Multi Splices:	0
Complexity:	0.04
Read Length, Minimum:	36
Read Length, Maximum:	36
Read Length, Average:	36.0
will treat all alignments as unique
testing for NH tags presence
file has NH tags
Will only consider alignments with 0 or less mismatches
will only consider + strand reads
region chrIII-NC_003074 0 23459830 not found in bam file, skipping
region chrII-NC_003071 0 19698289 not found in bam file, skipping
region chrI-NC_003070 0 30427671 not found in bam file, skipping
region chrIV-NC_003075 0 18585056 not found in bam file, skipping
region chrV-NC_003076 0 26975502 not found in bam file, skipping
found 2873853.0 reads
RPM normalization Factor = 2.873853