Whether or not normalizeUsingRPKM used not showing in log.

[endrebak]

endrebak@havpryd ~/c/p/w/tss> /local/home/endrebak/anaconda3/envs/py27/bin/bamCoverage --normalizeUsingRPKM -b data/tss/bam/filtered_Exp1_0h_H3K27me3.bam -o data/tss/bigwig/filtered_Exp1_0h_H3K27me3.bigwig
verbose: False
out_file_for_raw_data: None
numberOfSamples: None
bedFile: None
bamFilesList: ['data/tss/bam/filtered_Exp1_0h_H3K27me3.bam']
ignoreDuplicates: False
numberOfProcessors: 16
samFlag_exclude: None
save_data: False
blackList: None
stepSize: 50
smoothLength: None
center_read: False
defaultFragmentLength: read length
chrsToSkip: []
region: None
maxPairedFragmentLength: 1000
samFlag_include: None
binLength: 50
blackListFileName: None
minMappingQuality: None
zerosToNans: False

Hard to tell if it does normalize or not. Cannot see a corresponding True flag above.

[dpryan79]

It might be nice to add that. Currently the normalization occurs before the multithreaded step that prints that information, which is why it's not included.

[dpryan79]

In the 2.3.0 release, there will now be a normalization: depth/RPKM/1x line printed. Note that for things like bamCompare that this will be printed multiple times.