hicDifferentialTAD TypeError

[CriticalSci]

Hello, I'm having issues with hicDifferentialTAD for relatively large bin sizes. Domains are called with hicFindTADs without any problems. Sometimes it works, sometimes it doesn't. Seems to break for specific chromosome and bin size combinations.

• [x] Search whether this issue (or a similar issue) has been solved before using the search tab above. Link the previous issue if appropriate below. Could be related to #725

• [x] Paste your HiCExplorer version (hicInfo --version) and your python version (python --version) below. hicInfo 3.7.2 Python 3.10.12

• [x] Have you checked our documentation on hicexplorer.readthedocs.io? Yes

• [x] Do you use conda to install HiCExplorer? Yes

• [x] Do you use the latest HiCExplorer release? Yes

• [x] Paste the full HiCExplorer command that produces the issue below (ignore if you simply spotted the issue in the code/documentation).

  hicDifferentialTAD --targetMatrix prod/trgt_50K_NormRefCorr.h5 \
  --controlMatrix prod/ctrl_50K_NormRefCorr.h5 \
  --tadDomains prod/50K/chr2/ctrl_KR_FDR1_DELTA1_domains.bed \
  --outFileNamePrefix prod/50K/chr2/ctrl_KR_FDR1_DELTA1_P5 \
  --pValue 0.05 \
  --mode all \
  --modeReject one \
  --threads 12

• [x] Paste the output printed on screen from the command that produces the issue below (ignore if you simply spotted the issue in the code/documentation).

  ERROR:hicmatrix.HiCMatrix:Index error
  Traceback (most recent call last):
  File "/opt/anaconda3/envs/hicexplorer23/lib/python3.10/site-packages/hicmatrix/HiCMatrix.py", line 271, in getRegionBinRange
  endbin = sorted(self.interval_trees[chrname][endpos:endpos + 1])[0].data
  IndexError: list index out of range
  ERROR:hicexplorer.hicDifferentialTAD:'NoneType' object is not subscriptableTraceback (most recent call last):
  File "/opt/anaconda3/envs/hicexplorer23/lib/python3.10/site-packages/hicexplorer/hicDifferentialTAD.py", line 170, in computeDifferentialTADs
  outer_left_boundary_index_control = hic_matrix_control_inter_tad.getRegionBinRange(str(chromosom), start, end)[0]
  TypeError: 'NoneType' object is not subscriptable

[CriticalSci]

UPDATE:

I believe the issue originates from an incompatibility between the output of hicMergeMatrixBins and the processing in hicFindTADs and/or hicDifferentialTAD.

My current workaround is to generate the alternate resolutions directly from cooler allowing me to omit the hicMergeMatrixBins step.

1. hicMergeMatrixBins (skip)
2. hicNormalize
3. hicAdjustMatrix
4. hicCorrectMatrix
5. hicFindTADs
6. hicDifferentialTAD