#9 Possible fix for alt alleles mapped onto the negative strand

[Andrew Yates]

Hi. I have a possible bugfix for 0.3.3 for better handling inverted VCF mapping; a previously raised issue in this tracker. The patch allows CrossMap to detct if a VCF mapping was inverted, and if so reverse complements the altenerative allele. We at Ensembl have tested a similar bugfix on 0.2.8 (our internal installation version of CrossMap) and can confirm this now correctly reverse complements the allele.

I've attached the patch to this issue. You can also see it in our GitHub repository at https://github.com/Ensembl/CrossMap-Patch/blob/master/CrossMap-0.3.3.patch.

I'd appreciate your input on this matter and if it can be integrated into future CrossMap releases.

Thanks.

[Liguo Wang]

I have incorported this patch into v0.3.4 (https://sourceforge.net/projects/crossmap/files/). Please check if this version works as you expected.

[Andrew Yates]

I've passed 0.3.4 through a flipped position between 37 and 38. The alt allele reverse complements as expected. Thank you!

[Andrew Yates]

Also FYI you can close issue 2 as this bugfix resolves that issue