plotFingerprint results depend on BAM file order — input sorting needed

[QuentinDuvertCurie]

The output of plotFingerprint varies depending on the order of BAM files provided in the -b parameter, even when all other arguments remain identical. This affects both the plotted fingerprint and the raw/quality metrics outputs.

For example, the two following commands differ only in BAM and label order:

plotFingerprint -b ID1_filtered_shifted.bam ID2_filtered_shifted.bam ID3_filtered_shifted.bam \
                -plot bams_fingerprint.pdf \
                -p 1 \
                -l 'ID1'  'ID2'  'ID3' \
                --extendReads --skipZeros \
                --outRawCounts plotFingerprint.raw.txt \
                --outQualityMetrics plotFingerprint.qmetrics.txt

plotFingerprint -b ID3_filtered_shifted.bam ID2_filtered_shifted.bam ID1_filtered_shifted.bam \
                -plot bams_fingerprint.pdf \
                -p 1 \
                -l 'ID3'  'ID2'  'ID1' \
                --extendReads --skipZeros \
                --outRawCounts plotFingerprint.raw.txt \
                --outQualityMetrics plotFingerprint.qmetrics.txt

Yet, the output values are different (example below):

ex :

< ID1	0.09378069129010372	0.495037541644535	0.3139128094725511	0.0	0.8441872981700753	0.500194148356678	0.5780619843832019
< ID2	0.06696695249101738	0.49499669220481174	0.4336652314316469	0.0	0.8618137782561894	0.5026794267798673	0.610113953814954
< ID3	0.1291594430331159	0.4932775653633279	0.3207750269106566	1.966908847312887e-189	0.7711248654467169	0.5012198748086091	0.48126701308648095
---
> ID3	0.12720877527444388	0.49059151283469915	0.347135955831608	4.577699669843273e-96	0.7701863354037267	0.4925363505619147	0.4677414185704291
> ID2	0.0664847262121746	0.4928753619064219	0.4357487922705314	1.7808421833197564e-168	0.8542443064182195	0.5087629908428597	0.6063354668238865
> ID1	0.09515023035629501	0.49307920612922806	0.31815044858523117	1.2376769385685896e-178	0.8329882677708764	0.4997551395064236	0.5681266081275786

Version : deeptools 3.5.1