Rounding error when calculating number of reads from bam files?

[hackkr]

Hello!
Thanks for building such a streamlined tool for analyzing chromatin conformation capture data. I noticed a quirk when starting from bam files (--start-stage bam). It seems like calculation for number of reads in each bam file is off by an order of magnitude? I don't think that it affects any of the downstream processing, but wanted to report this.

hicstuff header:

INFO :: ## hicstuff: v3.2.3 log file
INFO :: ## date: 2024-06-18 12:42:29
INFO :: ## enzyme: AluI
INFO :: ## input1: /N/slate/rhackley/01_poreC_test/sup-output/paired_end/R1-renamed.bam 
INFO :: ## input2: /N/slate/rhackley/01_poreC_test/sup-output/paired_end/R2-renamed.bam
INFO :: The default output format is now `.cool`. The Hi-C matrix will be generated with cooler v0.10.0 (Abdennur & Mirny, Bioinformatics 2020).
INFO :: Checking content of bam files.
INFO :: 86725 reads found in each bam file.
INFO :: 86% reads (single ends) mapped with Q >= 30 (1483586/1734508)
INFO :: 741793 pairs successfully mapped (855.34%)

samtools flagstat R1.bam returns:

867254 + 0 in total (QC-passed reads + QC-failed reads)
867254 + 0 primary
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
867254 + 0 mapped (100.00% : N/A)
867254 + 0 primary mapped (100.00% : N/A)
867254 + 0 paired in sequencing
867254 + 0 read1
0 + 0 read2