requires 1 based coordinates for both start and finish.
This small fix includes a correction for that when parsing the -g options, as well a small check for a possible empty 'name' column (column[3]) where there may be further info in the bed file that could break the parsing (score - column[4] etc).
Please let me know if more requires changing. It would be great if these fixes could go out in a hotfix tagged release.
Hi,
I've noticed that the bed parsing is not correcting for bed format being 0-based start. Where
https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/util/Interval.html
requires 1 based coordinates for both start and finish.
This small fix includes a correction for that when parsing the -g options, as well a small check for a possible empty 'name' column (column[3]) where there may be further info in the bed file that could break the parsing (score - column[4] etc).
Please let me know if more requires changing. It would be great if these fixes could go out in a hotfix tagged release.
Kind regards,
davidrajones