computeMatrix.val.mat.gz files not zipped

[ivokwee]

Hi. The *.computeMatrix.val.mat.gz files in the deepTools module seem not to be zipped.

[drpatelh]

results
├── bwa
│   └── mergedLibrary
│       ├── deepTools
│       │   ├── plotFingerprint
│       │   │   ├── SPT5_T0_R1.plotFingerprint.pdf
│       │   │   ├── SPT5_T0_R1.plotFingerprint.qcmetrics.txt
│       │   │   ├── SPT5_T0_R1.plotFingerprint.raw.txt
│       │   └── plotProfile
│       │       ├── SPT5_T0_R1.computeMatrix.mat.gz
│       │       ├── SPT5_T0_R1.computeMatrix.vals.mat.gz
│       │       ├── SPT5_T0_R1.plotProfile.pdf

$ zcat SPT5_INPUT_R2.computeMatrix.vals.mat.gz | head
gzip: SPT5_INPUT_R2.computeMatrix.vals.mat.gz: not in gzip format

Yep, you are right @ivokwee 👍 Well spotted!! Ill fix that in the next release.

[ivokwee]

OK. Also, the first non-commented line of these computeMatrix.vals.mat.gz files has one column too many, so reading the vals.mat files give problems/warning in R.

genes:7080 SPT5_INPUT_R1.mLb.clN SPT5_INPUT_R1.mLb.clN

This could be resolved by either removing "genes:7080" from the column names header, or adding rownames (preferred) to the matrix values, I guess.

Thanks.

Ivo

[drpatelh]

Unfortunately, the format of the output file is something that I would be a little more reluctant to change because it's something that should be addressed upstream by deepTools or by scripts reading the file in - mainly for standardisation purposes. Happy to fix the naming convention though 👍

[drpatelh]

Fixed db3a364