Specifying genomic region has no effect

[martijnvermaat]

Maybe I'm doing something wrong, but it looks like the -region argument is ignored (other than parsing the region definition).

For example, specifying -region 'X:38000000..39000000' gives me the same result as specifying no region on full chromosome X alignments.

[arq5x]

Sorry, it is not yet implemented. Trivial to do, just haven't had the time yet. Will try to knock it out early next week.

[arq5x]

Actually, it is implemented, but I was confused about how it works (this is based upon bamtools, which I am not the primary developer of).

You specific a region as follows:

-region chr1:921474..922474

I suspect you might have used the following notation:

-region chr1:921474-922474

Note that the output will include flanking positions outside your region if there is >=1 read that overlaps your requested interval and extends into flanking positions.

[arq5x]

Commit e4d484c illustrates how to specify a region using bamtools syntax.

[martijnvermaat]

Thanks for looking at this! This indeed bit me at first.

However, the problem is something else. I have quite a few samples and listed them in a file for use with the -list argument. It seems -region is ignored when using the -listargument.