`d4tools create` builds empty d4 file for small input files

[pamelarussell]

I'm trying to build small D4 files to test my code, and have not been able to get d4tools create to successfully build a file from a small bedgraph or bigwig file: the D4 output is always empty. It does work for large public data files. Here is an example with a small bedgraph file.

I'm running version 0.3.4 installed from bioconda.

$ cat example1.bedgraph 
track type=bedGraph name="BedGraph Format" description="BedGraph format" visibility=full color=200,100,0 altColor=0,100,200 priority=20
chr1 49302000 49302300 1.0
chr1 49302300 49302600 0.75
chr1 49302600 49302900 0.50
chr1 49302900 49303200 0.25
chr1 49303200 49303500 0.0
chr1 49303500 49303800 0.25
chr1 49303800 49304100 0.50
chr1 49304100 49304400 0.75
chr1 49304400 49304700 1.00

$ cat chrom.sizes         
chr1    248956422
chr2    242193529
chr3    198295559
chr4    190214555
chr5    181538259
chr6    170805979
chr7    159345973
chr8    145138636
chr9    138394717
chr10   133797422
chr11   135086622
chr12   133275309
chr13   114364328
chr14   107043718
chr15   101991189
chr16   90338345
chr17   83257441
chr18   80373285
chr19   58617616
chr20   64444167
chr21   46709983
chr22   50818468
chrX    156040895
chrY    57227415
chrM    16569

$ d4tools create -g chrom.sizes example1.bedgraph
$ d4tools view example1.d4
chr1    0   248956422   0
chr2    0   242193529   0
chr3    0   198295559   0
chr4    0   190214555   0
chr5    0   181538259   0
chr6    0   170805979   0
chr7    0   159345973   0
chr8    0   145138636   0
chr9    0   138394717   0
chr10   0   133797422   0
chr11   0   135086622   0
chr12   0   133275309   0
chr13   0   114364328   0
chr14   0   107043718   0
chr15   0   101991189   0
chr16   0   90338345    0
chr17   0   83257441    0
chr18   0   80373285    0
chr19   0   58617616    0
chr20   0   64444167    0
chr21   0   46709983    0
chr22   0   50818468    0
chrX    0   156040895   0
chrY    0   57227415    0
chrM    0   16569   0

[38]

Hi @pamelarussell , thanks for reporting the issue.

I tried this locally, it seems you may have a file with space between fields - Please let me know if this is your case.

Thanks!

[pamelarussell]

Thanks! That was the problem. Would it be possible to fail with an informative message for an invalid input file?

[arq5x]

Yes, indeed. Also, D4 should support fractional values by default (it supports them but one has to invoke a flag). @38 is working on addressing both of these.

[38]

Hi @pamelarussell, just pushed the fix for this bug. Please let me know if there's anything still wrong.

This change will allow d4tools detect if the input needs to be fractional values automatically. Please let me know if this works on your side. Thanks!

[arq5x]

Does this work for you, @pamelarussell ?

[pamelarussell]

The latest fix does work for fractional values, thanks @arq5x and @38 !