deeptools / pyBigWig

A python extension for quick access to bigWig and bigBed files
MIT License
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addHeader does not support multiple calls #142

Open rlowe-altoslabs opened 1 year ago

rlowe-altoslabs commented 1 year ago

Not sure if this is intended or not but running addHeader multiple times seems to overwrite the existing header?

Example

import pyBigWig

with pyBigWig.open("example.bw", "w") as bw:
    header=[("chr1", 1000000), ("chr2", 1500000)]
    for item in header:
        bw.addHeader([item])
    items = [
        ["chr1", 0,5,0.0],
        ["chr1", 100,120,1.0],
        ["chr1", 125,126,200.0]
    ]
    for item in items:
        bw.addEntries([item[0]],[item[1]],ends=[item[2]],values=[item[3]])

Expected the above to work but instead fails on bw.addEntries with

RuntimeError: The entries you tried to add are out of order, precede already added entries, or otherwise use illegal values.

A couple of options in my opinion:

  1. Update docs and explicitly mention this behaviour
  2. Prevent addHeader being run a second time with some appropriate error
  3. Support this case. Reason the header is often read from a file and so the header could be added line by line. The addEntries supports this.

Obviously this is not hard to work around given one can create the list object and then call addHeader once complete.

wang3702 commented 1 month ago

Same error here. Also, the writing order of addEntries should follow the same order as we defined in bw.addHeader.