Error with bam2wig.py

[rspreafico]

Hello,

Congrats on this awesome, useful package! 

I have been running bam2wig.py and sometimes got an error like this:

Overlap on chr_16b between items starting at 1459 and 1459.

Please remove overlaps and try again

Overlap on chr_16b between items starting at 14610 and 14610.

Please remove overlaps and try again

I took wigToBigWig out of PATH, and no error was reported, indicating that this was output from wigToBigWig, and that the wig file generated by bam2wig.py had something wrong. However, when I manually called wigToBigWig on the wig file, no error was reported anymore. When I restored wigToBigWig into the PATH, and then called bam2wig.py, the same error popped out. 

So I took a look at SAM.py and noticed that the connection to wig files was not closed after finishing writing, and before calling wigToBigWig. So I introduced the following chunk of code after line 2616:

FWO.close()

if len(strandRule) != 0:

RVO.close()

And reinstalled RSeQC. Tried again to call bam2wig.py, and this time it worked. I am not sure whether this is the best fix and the actual reason for the error I got, but it may be worth investigating in view of the next release. 

Thank you,

Roberto

[Liguo Wang]

Hi Roberto,

Thanks for identifying this bug. Yes, your fix is perfect. We will update the code.

Liguo

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