pyBigWig
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addHeader does not support multiple calls
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:
- Update docs and explicitly mention this behaviour
- Prevent
addHeader
being run a second time with some appropriate error - 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.