Running Bedops 2.4.14 on Mac OS 10.8.5. Having problems with the following command:
bedops -n 2 RNAPII.USHP.all mask.txt > RNAPII.USHP.masked
The script runs without error. However, for some reason, the very last interval of my mask.txt file is being ignored by this function. The interval is chrY:59034017-59034077, and is preceded by 1,000,000 other intervals, correctly sorted, and including other intervals on the Y chromosome. The -n function removes everything as expected EXCEPT this very last interval. Puzzled as to why this would be the case. If instead I try the following
bedops --element-of 2 RNAPII.USHP.all mask.txt > intersectwithmask.bed
then I see everything as expected, including the intersecting intervals for the chrY:59034017-59034077 region in the RNAPII.USHP.all bed file. So this is not an issue with data already being absent from the reference file, or a data corruption issue in the mask.txt file.