Get complete mate position

[Victorin Martin]

Hi,

First of all Thanks Derek for BamTools :-).
I'm a new user and I'm still trying to grasp all the power of the API.

I'm currently using it on RNA-seq paired-end reads. I was wondering what is the simplest way to get the complete genomic position of a mate read.
MatePosition is of course directly available but I'd like to access the output of GetEndPosition() called on the mate of the current read.
Is there any way to do so?

I thought about sorting the bam file by name to get mates as successive reads in the Bam file but, since there is no real name convention for the reads, I doubt this is a good idea.

Thanks!

Victorin.

[Lawrence Ganeshalingam]

Victorin

I contemplating in using this tool. I'm a new user as well. I'm wondering, if you ever got a response to your question? Basically I'm trying to understand that if the Author or any other power users are very sportive in this forum. I appreciate your response.

thanks,
Lawrence

[Adam Roberts]

You can look at how I do it here: https://github.com/adarob/eXpress/blob/master/src/mapparser.cpp

Unfortunately there is no straightforward way to do it efficiently if you are parsing the full file.

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